bioinformatics

<BODY> <TITLE>bioinformatics</TITLE> <META http-equiv=Content-Type content="text/html; charset=windows-1252"> <META content=webmaster@bioinformatics.vg name=OWNER> <META content=webmaster@bioinformatics.vg name=AUTHOR> <META CONTENT="bioinformatics portal" NAME="bioinformatics"> <META http-equiv=CONTENT-LANGUAGE content=English> <META http-equiv="VW96.OBJECT TYPE" content=Homepage> <META http-equiv=pragma content=nocache> <META http-equiv=expires content="Mon, 1 October 2000 00:00:01 PST"> <META content=INDEX,FOLLOW name=ROBOTS> <META content="MSHTML 5.50.4134.100" name=GENERATOR> <META content="bioinformatics" name=Description> <META content="bioinformatics biotechnology genomics genbank molecular biology software ebi, bioinformatics tools, embl ncbi gene genomics protein promoter, alignment bioinformatics, nucleotide fasta blast protein sequence translation restriction free analysis" name=Keywords><LINK href="style.css" type=text/css rel=STYLESHEET> <BODY bgProperties=fixed bgColor=#ffffff background=Images/Image1.jpg><BASE target=_blank><BR> <BR> <h1>Please go to the new page for a current <a HREF="http://www.bioinformatics.vg">bioinformatics</a> links database</h1> <TABLE> <TBODY> <TR> <TD vAlign=top>  <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=3> <H4 align=center><FONT size=2>Sequence manipulation bioinformatics tools</H4></TD></TR> <TR> <TD>  <A title="University of Oxford web-based sequence analysis suite including more than 100 programs" href="http://analysis.molbiol.ox.ac.uk/pise_html/index.html">OUBC</A></TD> <TD> </TD> <TD align=right>      <A href="http://bioweb.pasteur.fr/intro-uk.html">Pasteur Institute</A> </TD></TR> <TR> <TD>  <A title="BCM provides CAP Sequence Assembly and many other Sequence Utilities" href="http://searchlauncher.bcm.tmc.edu/">BCM</A></TD> <TD><A title="Detection of Frameshift Sequencing Errors by Comparison of Nucleic Acid Sequence Data with Expected Protein Sequence" href="http://www.bork.embl-heidelberg.de/ERR_WISE/"></A></TD> <TD align=right>  <A title="SEquence analysis using WEb Resources" href="http://iubio.bio.indiana.edu/webapps/SeWeR/">SeWer</A> </TD></TR> <TR> <TD>  <A title="MolBiol.Net's reverse complement tools - the only one that copes with degenerate sequence" target=middleright href="../bioinformatics_tools/reversecomplement.htm">Reverse comp</A></TD> <TD> </TD> <TD align=right> <A title="Downloadable JAVA Biological sequence editor and analysis program, including links to network services and external analysis programs" href="http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/">SeqPup</A> </TD></TR> <TR> <TD>  <A href="http://www.ualberta.ca/~stothard/javascript/rev_comp.html">Reverse comp</A></TD> <TD> </TD> <TD align=right><A href="http://www.ualberta.ca/~stothard/javascript/index.html">Seq manipulation </A> </TD></TR> <TR> <TD>  <A title="MolBiol.Net's reverse translation of protein to degenerate DNA sequence tool" href="../bioinformatics_tools/reversetranslate.htm">Rev translate</A></TD> <TD></TD> <TD align=right><A title="Contig DNA sequence assembly program at Lyon, Huang and Madan" target="" href="http://pbil.univ-lyon1.fr/cap3.html">CAP3</A> </TD></TR> <TR> <TD>  <A title="Sequence format converstion: converts input DNA/AA sequence to specified formay. Input format is determined automatically." href="http://bimas.dcrt.nih.gov/molbio/readseq/">ReadSeq</A></TD> <TD></TD> <TD align=right>  <A title="Detection of Frameshift Sequencing Errors by Comparison of Nucleic Acid Sequence Data with Expected Protein Sequence" href="http://www.bork.embl-heidelberg.de/ERR_WISE/">ERR_WISE</A> </TD></TR> <TR> <TD>  </TD> <TD></TD> <TD align=right><A title="Protein to nucleotide backtranslation by Entelechon" href="http://www.entelechon.com/eng/backtranslation.html">Backtranslate</A> </TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=institutes></A> <H4 align=center>Translation of DNA to protein bioinformatics</H4></TD></TR> <TR> <TD>  <A title="MolBiol.Net Translation Tool - featuring 10 alternative codon tables and sequence security" href="../bioinformatics_tools/tranlatetool.htm">Translate Tool</A></TD></TR> <TR> <TD>  <A title="Translate program by Shultz" href="http://biocommons.bcc.washington.edu/services/psoftware/dnatranslator/index.html">DNA Sequence Translation</A></TD></TR> <TR> <TD>  <A href="http://www.expasy.ch/tools/dna.html">ExPASy - tranlate tool</A></TD></TR> <TR> <TD>  <A title="EBI translate tool" href="http://www2.ebi.ac.uk/translate/">Translation Machine</A></TD></TR> <TR> <TD>  <A title="Translate program at Lundberg" href="http://bio.lundberg.gu.se/edu/translat.html">DNA to protein translation</A></TD></TR> <TR> <TD>  <A title="Unfortunately now requires registration" href="http://mbshortcuts.com/translator/">MBS translator</A></TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef background=img/background.jpg border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=institutes></A> <H4 align=center> Restriction Analysis </H4></TD></TR> <TR> <TD>  <A title="Restriction map DNA sequences using WebCutter" href="http://www.ccsi.com/firstmarket/cutter/cut2.html">Webcutter</A></TD></TR> <TR> <TD>  <A href="http://tools.neb.com/NEBcutter/index.php3">NEBcutter</A> </TD></TR> <TR> <TD>  <A title="Finds restriction endonuclease cleavage sites in DNA sequences, supports linear and circular DNA and provides several ways to sort and filter output" href="http://www.restrictionmapper.org">Restriction mapper</A></TD></TR> <TR> <TD>  <A title="Recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data" href="http://rebase.neb.com">Rebase</A></TD></TR> <TR> <TD>  </TD></TR></TBODY></TABLE><BR> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=retrieval></A> <H4 align=center>Sequence retrieval </H4></TD></TR> <TR> <TD>  <A title="Ultimate sequence retrieval system" href="http://srs.ebi.ac.uk">SRS session </A></TD></TR> <TR> <TD>  <A href="http://www.ncbi.nlm.nih.gov/Entrez/">Entrez</A></TD></TR> <TR> <TD>  <A title="Gene Finder Based on Generalized Hidden Markov Models" href="http://www.fruitfly.org/seq_tools/genie.html">HMM Genie</A></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef background=img/background.jpg border=0> <TBODY> <TR bgColor=#e6e6fa> <TD> <H4 align=center>Primer design bioinformatics</H4> <H4></H4></TD></TR> <TR> <TD>  <A title="Calculates the possible permutations and energies of a single primer forming dimers and hairpin loops (self-complimentarity) with itself allowing users to assess primers that they have designed themsevles" href="http://207.32.43.248/oligocalc.asp">Oligo Analyzer2.5</A></TD></TR> <TR> <TD>  <A title="Calculates the melting temperature of an oligonucleotide" href="http://members.aol.com/_ht_a/lucatoldo/myhomepage/JaMBW/3/1/9/index.html">Oligo Calculator</A></TD></TR> <TR> <TD>  <A title="User friendly java primer design, slow to load but comprehensive" href="http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html">NetPrimer</A></TD></TR> <TR> <TD>  <A title="MethPrimer - Design Primers for Methylation PCRs by Long-Cheng Li, M.D. of Urology Research Dept at VA Medical Center and UCSF San Francisco. The only free public methylation primer program available on the net" href="http://itsa.ucsf.edu/~urolab/methprimer/">Methprimer</A></TD></TR> <TR> <TD>  <A title="Picks decent primers from a DNA sequence" href="http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi">Primer3</A></TD></TR> <TR> <TD>  <A title="Design of sequencing or PCR primers" href="http://genome-www2.stanford.edu/cgi-bin/SGD/web-primer">WebPrimer</A> </TD></TR> <TR> <TD>  <A title="Includes link to pairwise primer analysis program" href="http://eatworms.swmed.edu/~tim/primerfinder/">PrimerFinder</A></TD></TR> <TR> <TD>  <A title="Downloadable PCR primer design program for Windows by Ruslan Kalendar of the Institue of Biotechnology, Helsinki, Finland" href="http://www.biocenter.helsinki.fi/bi/bare-1_html/oligos.htm">Primer9</A></TD></TR> <TR> <TD>  <A title="Version 1.05" href="http://nmr.kaist.ac.kr/shbae/pub/oligo2002/Oligo2002v105.html">Oligo2002</A></TD></TR> <TR> <TD>  <A title="Large scale design of sequence primers especially for walking" href="http://pride.molgen.mpg.de/pride.html">Pride</A> or <A title="Designs PCR primers or oligos (50-70mers) used for DNA chips" href="http://pride.molgen.mpg.de/genomepride.html">GenomePride</A></TD></TR> <TR> <TD>  <A title="Downloadable PCR primer design program (1.5MB) by Ruslan Kalendar of the Institute of Biotechnology, Helsinki, Finland" href="http://www.biocenter.helsinki.fi/bi/bare-1_html/oligos.htm">Oligos (download)</A></TD></TR> <TR> <TD>  <A title="Degenerate PCR primers designed from protein multiple sequence alignments" href="http://blocks.fhcrc.org/blocks/codehop.html">Codehop</A> <INPUT onmouseover="event.srcElement.style.backgroundColor='e6e6fa'" title="Tutorial on degenerate PCR primer design" style="FONT-SIZE: 8px; CURSOR: help; BACKGROUND-COLOR: #ffffe0" onclick="window.open('http://www.dartmouth.edu/artsci/bio/ambros/protocols/other/koelle/degenerate_PCR.html')" onmouseout="event.srcElement.style.backgroundColor='ffffe0'" type=button value=Help></TD></TR> <TR> <TD align=right><A title="Web Guide for Polymerase Chain Reaction Technique" href="http://www.pcrlinks.com">PCRlinks.com </A></TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=2> <H4 align=center>Alignment bioinformatics</H4></TD></TR> <TR bgColor=#ffffe0> <TD> <P align=center> <STRONG>Tools </STRONG></P></TD> <TD> <P align=center><STRONG>  Viewers and editors</STRONG></P></TD></TR> <TR> <TD>  <A title="Gold standard alignment tool" href="http://www.ebi.ac.uk/clustalw/">ClustalW</A>  </TD> <TD>  <A href="http://bioweb.pasteur.fr/seqanal/interfaces/boxshade-simple.html">Boxshade</A> or <A title="Pretty Printing and Shading of Multiple-Alignment files" href="http://www.ch.embnet.org/software/BOX_form.html">Boxshade </A></TD></TR> <TR> <TD>  <A title="Allows sequence search against protein families database of alignments and HMMs
" href="http://www.sanger.ac.uk/Software/Pfam/search.shtml">Pfam</A></TD> <TD>  <A title="CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication (requires software download)" href="http://www.lg.ndirect.co.uk/chroma/">Chroma</A><A href="http://genomatix.gsf.de/cgi-bin/dialign/dialign.pl"></A></TD></TR> <TR> <TD>  <A href="http://alces.med.umn.edu/">Alces</A></TD> <TD>  <A title="Downloadable multiple sequence alignment editor" href="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/seaviewWin95.exe">Seaview</A></TD></TR> <TR> <TD>  <A title="Global alignment between two sequences which includes percentage identity" href="http://analysis.molbiol.ox.ac.uk/pise_html/stretcher.html">Stretcher</A></TD> <TD>  <A title="Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows" href="http://www.psc.edu/biomed/genedoc/">GeneDoc</A></TD></TR> <TR> <TD>  <A target="" href="http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/dialign_submit">DiAlign</A></TD> <TD><A href="http://alces.med.umn.edu/"></A></TD></TR> <TR> <TD>  <A title="Divide-and-Conquer Multiple Sequence Alignment" href="http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/dca_submit">DCA</A></TD> <TD bgColor=#ffffe0> <P align=center>  <STRONG>Whole genome alignment bioinformatics</STRONG></P></TD></TR> <TR> <TD>  <A href="http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html">Multi align resource</A></TD> <TD>  <A title="Fast Local Alignment of Gigabases" href="http://flag.itri.org.tw/">FLAG</A><A href="http://bioweb.pasteur.fr/seqanal/interfaces/boxshade-simple.html"></A></TD></TR> <TR> <TD>  <A title="Consistency based multiple alignment method" href="http://www.cmbi.kun.nl/bioinf/tools/T_COFFEE/">T-Coffee</A></TD> <TD>  <A href="http://www-gsd.lbl.gov/ids-bin/VistaInput">Vista</A></TD></TR> <TR> <TD>  <A title="SIM4 addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors" href="http://biom3.univ-lyon1.fr/sim4.html">SIM4</A></TD> <TD>  <A title="Aligning two multimegabyte-size sequences" href="http://www.softberry.com/berry.phtml?topic=scanh&prg=SCAN2">Scan2</A></TD></TR> <TR> <TD>  <A title="Align and detect conserved regions in long genomic sequences" href="http://www-gsd.lbl.gov/VISTA/">VISTA</A></TD> <TD>  <A title="Map your sequence to Human genome draft for a second" href="http://www.softberry.com/berry.phtml?topic=showmap">FMAP</A></TD></TR> <TR> <TD>  <A title="Align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools" href="http://www.sanger.ac.uk/Software/Wise2/">Wise2</A></TD> <TD align=middle bgColor=#ffffe0><STRONG>Pairwise alignment </STRONG></TD></TR> <TR> <TD>  <A title="Spidey is an mRNA-to-genomic alignment program" href="http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/index.html">Spidey</A></TD> <TD>  <A title="Uses the blast algorithm to align two sequences" href="http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html">Blast Two Sequences</A></TD></TR> <TR> <TD>  <A title="PipMaker aligns two DNA sequences and returns a percent identity plot of that alignment, together with a traditional textual form of the alignment" href="http://bio.cse.psu.edu/cgi-bin/pipmaker?basic">PipMaker</A></TD> <TD>  <A title="Use this tool for pairwise alignment, ie. 2 sequences only" href="http://www.ebi.ac.uk/emboss/align/">Align</A></TD></TR> <TR> <TD>  <A title="SIM - Alignment Tool for protein sequences" href="http://ca.expasy.org/tools/sim-prot.html">Sim-Prot</A></TD> <TD></TD></TR> <TR> <TD>  <A title="Align a sequence to its ortholog in the human genome" href="http://pipeline.lbl.gov/cgi-bin/mygodzilla">myGodzilla</A></TD> <TD></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef background=img/background.jpg border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=2> <H4 align=center>Protein Structure bioinformatics</H4></TD></TR> <TR> <TD vAlign=top> <TABLE cellSpacing=0 cellPadding=0 width="100%" border=0 VALIGN="TOP"> <TBODY> <TR> <TD vAlign=top align=middle bgColor=#ffffe0><STRONG>3D Structure Tools</STRONG></TD></TR> <TR> <TD>  <A title="Unique worldwide repository for the processing and distribution of 3-D biological macromolecular structure data." href="http://pdb.ccdc.cam.ac.uk/pdb/">Protein Data Bank </A></TD></TR> <TR> <TD vAlign=top>  <A title="MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations." href="http://www.avatar.se/molscript/">MolScript</A></TD></TR> <TR> <TD>  <A title="Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware." href="http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3D</A></TD></TR> <TR> <TD>  <A title="Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service" href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</A></TD></TR> <TR> <TD>  <A title="Open-source freeware molecular visualisation tool developed in Java" href="http://www.adcworks.com/ContentManager.jsp?cid=31">Java3D</A></TD></TR> <TR> <TD>  <A title="Fully automated protein structure homology-modeling server" href="http://www.expasy.ch/swissmod/">Swiss-Model</A> </TD></TR> <TR> <TD>  <A title="User friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts" href="http://www.expasy.ch/spdbv/">Deep view</A></TD></TR> <TR> <TD>  <A title="Predicts the structure of proteins from the sequence : secondary, local, supersecondary, and tertiary" href="http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.html">HMMSTR/Rosetta </A></TD></TR> <TR> <TD>  <A title="The UCLA DOE Fold Recognition server is a new project which aims to help in the computational analysis and prediction of structure from amino acid sequences" href="http://www.doe-mbi.ucla.edu/~frsvr/frsvr.html">FRSVR</A></TD></TR> <TR> <TD>  <A href="http://www.cse.ucsc.edu/research/compbio/HMM-apps/model-library-search.html">SAMt98</A></TD></TR> <TR> <TD>  <A title="The DOE FOLD Server - easy to register for free" href="http://fold.doe-mbi.ucla.edu/">UCLA / DOE</A></TD></TR> <TR> <TD>  <A title="Structural classification of proteins - provides a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known" href="http://scop.mrc-lmb.cam.ac.uk/scop/">SCOP</A></TD></TR> <TR> <TD>  <A title="The CPHmodels World Wide Web server predict protein structure using comparative (homology) modelling" href="http://www.cbs.dtu.dk/services/CPHmodels/">CPH-Models </A></TD></TR> <TR> <TD>  <A title="Jackal is a protein structure modeling package with capabilities in: protein homology modeling, side-chain and loop prediction/mutation, reconstruction of missing residues/atoms in protein structure, protein structure manipulation" href="http://trantor.bioc.columbia.edu/~xiang/jackal/">Jackal</A></TD></TR> <TR> <TD>  <A href="http://genomic.sanger.ac.uk/123D/123D.html">123D Sanger</A></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE cellSpacing=0 cellPadding=0 width="100%" border=0 VALIGN="TOP"> <TBODY vAlign=top> <TR> <TD vAlign=top bgColor=#ffffe0><STRONG>3D Structure Viewers</STRONG></TD></TR> <TR> <TD>  <A title="Open Source Rasmol Homepage - RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in 1992" href="http://openrasmol.org/">RasMol</A> and <A href="http://info.bio.cmu.edu/Courses/BiochemMols/RasMolTutorial/RasTut.html">tutorial</A></TD></TR> <TR> <TD>  <A title="You must register with MDL before downloading this free 3D modelling plugin" href="http://www.mdlchime.com/chime/">Chime</A></TD></TR></TBODY></TABLE><BR> <TABLE cellSpacing=0 cellPadding=0 width="100%" border=0 VALIGN="TOP"> <TBODY> <TR> <TD vAlign=top bgColor=#ffffe0> <P align=center><STRONG>Secondary Structure bioinformatics</STRONG></P></TD></TR> <TR> <TD>  <A title="Protein secondary structure prediction" href="http://jura.ebi.ac.uk:8888/">Jpred2</A></TD></TR> <TR> <TD>  <A title="Protein secondary structure prediction (& transmembrane helix prediction & tertiary structure prediction by threading)" href="http://insulin.brunel.ac.uk/psipred/">PsiPred</A></TD></TR> <TR> <TD>  <A title="Homology-derived Secondary Structure of Proteins" href="http://zlab.bu.edu/k2">HSSP</A></TD></TR> <TR> <TD>  <A title="Defines secondary structure and solvent exposure from 3D coordinates" href="http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html">DSSP db</A></TD></TR> <TR> <TD>  <A title="Protein structure alignment" href="http://zlab.bu.edu/k2">K2</A></TD></TR></TBODY></TABLE></TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=phylogeny></A> <H4 align=center>Phylogeny bioinformatics tools </H4></TD></TR> <TR> <TD>  <A href="http://sdmc.krdl.org.sg:8080/~lxzhang/phylip/">Phylip (Singapore)</A></TD></TR> <TR> <TD>  <A href="http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html">Phylip (Pasteur)</A></TD></TR> <TR> <TD>  <A href="http://bioweb.pasteur.fr/seqanal/interfaces/fastdnaml.html">FastDNAml</A></TD></TR> <TR> <TD>  <A target="" href="http://cbrg.inf.ethz.ch/Server/subsection3_1_6.html">TreeGen</A></TD></TR> <TR> <TD>  <A href="http://www.genebee.msu.su/services/phtree_reduced.html">Phylogenetic tree prediction</A></TD></TR> <TR> <TD>  <A href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">Treeview</A></TD></TR> <TR> <TD>  <A href="http://iubio.bio.indiana.edu/treeapp/">Phylodendron</A></TD></TR> <TR> <TD> </TD></TR> <TR> <TD> </TD></TR></TBODY></TABLE><BR> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef background=img/background.jpg border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=2> <H4 align=center>Gene identification bioinformatics</H4> <H4></H4></TD></TR> <TR bgColor=#ffffe0> <TD align=middle>  Intron/Exon<BR>prediction</TD> <TD align=middle>  ORF identification<BR>and miscellaneous</TD></TR> <TR> <TD>  <A title="This server provides access to the program GenomeScan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms." href="http://genes.mit.edu/genomescan.html"><FONT GenomeScan</A></TD> <TD><FONT   <A title="Coding probability of single exons, Gene Recognition and Assembly Internet Link" href="http://compbio.ornl.gov/Grail-1.3/"><FONT X-Grail</A></TD></TR> <TR> <TD><FONT   <A title="Splice site prediction, trained on C.elegans and A.thaliana (used to be called NetPlantGene2)" href="http://www.cbs.dtu.dk/services/NetGene2/"><FONT NetGene2 </A></TD> <TD><FONT   <A title="Coding probability of single exon, Borodovsky and Lukashin" href="http://genemark.biology.gatech.edu/GeneMark/hum.cgi"><FONT GeneMark</A><FONT  (<A href="http://www2.ebi.ac.uk/genemark/"><FONT alt</A><FONT )</TD></TR> <TR> <TD><FONT   <A href="http://www.cbs.dtu.dk/services/NetPGene/"><FONT NetPlantGene</A></TD> <TD><FONT   <A target="" href="http://genomic.sanger.ac.uk/gf/gf.html"><FONT Genefinder</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A href="http://rgp.dna.affrc.go.jp/RiceHMM/"><FONT RiceHMM</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A title="Tools for prediction and analysis of protein-coding gene structure" href="http://www.itba.mi.cnr.it/webgene/"><FONT WebGene</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A title="Gene modelling, US" href="http://genes.mit.edu/GENSCAN.html"><FONT GenScan</A><FONT  <A title="Gene modelling, Europe" href="http://genome.dkfz-heidelberg.de/cgi-bin/GENSCAN/genscan.cgi"><FONT GenScan</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A onmouseover="self.status='Wise2 comparison allows the simultaneous prediction of gene structure & homology based alignment';return true" title="Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors" href="http://www.sanger.ac.uk/Software/Wise2/genewiseform.shtml"><FONT Wise2</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A title="Rapidly identify minimum ORF size and display graphically and textually" href="http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl"><FONT FramePlot</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A href="http://www.ncbi.nlm.nih.gov/gorf/gorf.html"><FONT ORF Finder</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A href="http://125.itba.mi.cnr.it/~webgene/wwwgene.html?"><FONT GenView</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A title="Rapid identification of proteins based upon fast probabilistic analysis of sequence function using scoring matrices" href="http://dna.stanford.edu/ematrix/ematrix-search.html"><FONT E-Matrix</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A href="http://l25.itba.mi.cnr.it/~webgene/genebuilder.html"><FONT GeneBuilder</A></TD></TR> <TR> <TD><FONT </TD> <TD><FONT   <A title="Dictionary driven microbial gene finding" href="http://cbcsrv.watson.ibm.com/Tgi.html"><FONT DMGF</A></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=2> <H4 align=center>Sequence search bioinformatics</H4> <H4></H4></TD></TR> <TR> <TD vAlign=top> <TABLE width="100%" align=center VALIGN="TOP"> <TBODY> <TR> <TD bgColor=#ffffe0><B> Blast Tools</B></TD></TR> <TR> <TD><A title="Washington University blast2 (blast 2.0 with gaps)" href="http://www.ebi.ac.uk/blast2"> WU-Blast2</A></TD></TR> <TR> <TD><A title="NCBI blast2 (blastall) program" href="http://www.ebi.ac.uk/blastall"> NCBI-BlastAll</A></TD></TR> <TR> <TD><A title="European blast2 Vector Searches. Check your sequences for vector contamination" href="http://www.ebi.ac.uk/blastall/vectors.html"> Blast2 EVEC</A></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Tabular&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&NCBI_GI=on&PAGE=MegaBlast&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes"> Megablast</A></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&CDD_SEARCH=on&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes"> PSI and PHI blast</A></TD></TR> <TR> <TD><A title="Analysis of immunoglobulin sequences in GenBank" href="http://www.ncbi.nlm.nih.gov/igblast/"> IgBlast</A></TD></TR> <TR> <TD><A title="Blast server of EST clusters and alignments based on the EuroGeneIndexes" href="http://www.ebi.ac.uk/EGIblast2"> EGI blast</A></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE width="100%" align=center VALIGN="TOP"> <TBODY> <TR> <TD bgColor=#ffffe0><B> Other bioinformatics Tools</B></TD></TR> <TR> <TD><A title="Rapidly compares a protein sequence to a protein database, or a DNA sequence to a DNA library" href="http://www.ebi.ac.uk/fasta33/"> Fasta3</A>  or <A href="http://fasta.genome.ad.jp/"> Fasta</A></TD></TR> <TR> <TD><A href="http://www.dna.affrc.go.jp/htbin/tswn.pl"> Smith-Waterman Reverse Frame Search</A></TD></TR> <TR> <TD><A href="http://www.hgmp.mrc.ac.uk/ESTBlast/"> ESTblast</A></TD></TR> <TR> <TD><A title="Resources for UnTranslated Region Analysis" href="http://bighost.area.ba.cnr.it/BIG/UTRHome/"> UTR home page</A></TD></TR> <TR> <TD><A href="http://genome.dkfz-heidelberg.de/genweb/"> BIC</A></TD></TR> <TR> <TD><A title="Smith/Waterman bioinformatics type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH" href="http://www.ch.embnet.org/software/FDF_form.html"> FDF</A></TD></TR> <TR> <TD><A href="http://pir.georgetown.edu/iproclass/"> iPROCLASS</A></TD></TR> <TR> <TD> <P><A title="Blast2 service from EMBnet" href="http://www.ch.embnet.org/software/aBLAST.html"> Advanced BLAST</A></P></TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <TABLE width="100%" align=center VALIGN="TOP"> <TBODY> <TR> <TD bgColor=#ffffe0 colSpan=2><B> Blast by Genome Bioinformatics Tools</B></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsBlast.html&&ORG=Hs"> Human</A></TD> <TD> <P align=right><A href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/ara.html"> Arabidopsis</A></P></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/genome/seq/MmBlast.html"> Mouse</A></TD> <TD> <P align=right><A href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/riceWGS.html"> Rice</A></P></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/genome/seq/RnBlast.html"> Rat</A></TD> <TD> <P align=right><A href="http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi?organism=euk"> Other eukaryotes</A></P></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/fugu.html"> Fugu</A></TD> <TD> <P align=right><A href="http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi"> Microbial Genomes</A></P></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/genome/seq/DrBlast.html"> Zebrafish</A></TD> <TD> <P align=right><A href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/agambiae.html"> Anopheles</A></P></TD></TR> <TR> <TD> </TD> <TD> <P align=right><A title="Parasite Genomes blast server" href="http://www.ebi.ac.uk/blast2/parasites.html"> Parasites blast</A></P></TD></TR> <TR> <TD><A href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/agambiae.html"> </A></TD> <TD><A title="Parasite Genomes blast server" href="http://www.ebi.ac.uk/blast2/parasites.html"> </A></TD></TR> <TR> <TD> </TD> <TD><A href="http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi"> </A></TD></TR> <TR> <TD> </TD> <TD> </TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE width="100%" align=center VALIGN="TOP"> <TBODY> <TR> <TD bgColor=#ffffe0><B> NCBI blast bioinformatics tools</B></TD></TR> <TR> <TD><A title="Standard nucleotide-nucleotide BLAST" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&NCBI_GI=on&PAGE=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes"> BlastN</A></TD></TR> <TR> <TD><A title="Standard protein-protein BLAST" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes"> BlastP</A></TD></TR> <TR> <TD><A title="Nucleotide query - Protein database" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=1&NCBI_GI=on&PAGE=Translations&PROGRAM=blastx&SERVICE=plain&SET_DEFAULTS.x=37&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=no&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes"> BlastX</A></TD></TR> <TR> <TD><A title="Protein query - Translated nucleotides database " href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=0&NCBI_GI=on&PAGE=Translations&PROGRAM=tblastn&SERVICE=plain&SET_DEFAULTS.x=23&SET_DEFAULTS.y=10&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=no&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes"> TblastN</A></TD></TR> <TR> <TD><A title="Nucleotide query - Translated database" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=1&NCBI_GI=on&PAGE=Translations&PROGRAM=tblastx&SERVICE=plain&SET_DEFAULTS.x=21&SET_DEFAULTS.y=9&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=yes&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes"> TblastX</A></TD></TR> <TR> <TD><A title="Search the Conserved Domain Database using RPS-BLAST" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi"> RPS-blast</A></TD></TR></TBODY></TABLE></TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD vAlign=top> <H4 align=center>Signal scanner bioinformatics</H4></TD></TR> <TR> <TD>   <A title="Pol3scan recognizes the eukaryotic internal control regions A box and B box that are typical of tRNA genes and tDNA-derived elements" href="http://irisbioc.bio.unipr.it/pol3scan.html"> Pol3Scan</A></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef background=img/background.jpg border=0> <TBODY> <TR> <TD>  <A href="http://www.cse.ucsc.edu/~kent/improbizer/improbizer.html"> Improbizer</A>  (dynamic)</TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> </TD> <TD> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=features></A> <H4 align=center>Sequence features bioinformatics</H4></TD></TR> <TR> <TD>  <A title="Prediction of translation start site by neural net" href="http://www.cbs.dtu.dk/services/NetStart/">Start codon</A></TD></TR> <TR> <TD>  <A title="Predict poly(A) signals" href="http://125.itba.mi.cnr.it/~webgene/wwwHC_polya.html?"> polyAH</A> <A href="http://genomic.sanger.ac.uk/gf/gf.shtml"> polyAH</A></TD></TR> <TR> <TD>  <A title="Plots GC content over large sequences" href="http://analysis.molbiol.ox.ac.uk/pise_html/isochore.html"> Isochore</A></TD></TR> <TR> <TD>  <A title="Calculates the fractional GC content of nucleic acid sequences" href="http://analysis.molbiol.ox.ac.uk/pise_html/geecee.html"> %GC</A> or <A title="FREQSQ calculates the frequencies (number and percentage) of each base, their dinucleotides, codons or amino acids of a nucleic acid sequence" href="http://www.infobiogen.fr/services/analyseq/cgi-bin/freqsq_in.pl"> FreqSQ</A></TD></TR> <TR> <TD>  <A title="Screen for vector-derived sequence contamination in nucleic acid sequence" href="http://www.ncbi.nlm.nih.gov/VecScreen/"> VecScreen</A></TD></TR> <TR> <TD>  <A title="Prediction of protein coding regions, Exons, Pol II promoters, CpG islands, Islands,PolyA Sites and Repetitive DNA Elements" href="http://compbio.ornl.gov/Grail-bin/EmptyGrailForm/"> Grail (ORNL)</A></TD></TR> <TR> <TD bgColor=#ffffe0> <STRONG>Codon Usage</STRONG></TD></TR> <TR> <TD>  <A title="Codon Usage Database is an extended WWW version of CUTG (Codon Usage Tabulated from GenBank). The frequency of codon use in each organism is made searchable through this World Wide Web site." href="http://www.kazusa.or.jp/codon/">Codon Usage Tables</A></TD></TR> <TR> <TD>  <A title="Compilation of a sequence into a codon usage table" href="http://www.kazusa.or.jp/codon/countcodon.html"> CountCodon</A></TD></TR> <TR> <TD>  <A title="Analysis of Codon Usage (Peden)" href="http://bioweb.pasteur.fr/seqanal/interfaces/codonw.html"> Codon usage</A></TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD> <H4 align=center>Physico-chemical properties of proteins and RNA</H4></TD></TR> <TR> <TD>  <A target="" href="http://members.aol.com/_ht_a/lucatoldo/myhomepage/JaMBW/3/1/6/index.html"> Isoelectric point </A></TD></TR> <TR> <TD>  <A href="http://www-camis.stanford.edu/projects/helix/sstruct/"> RNA secondary structure </A></TD></TR> <TR> <TD>  <A href="http://ca.expasy.org/tools/peptide-mass.html"> Peptide mass calculator</A></TD></TR> <TR> <TD>  <A href="http://www.matrixscience.com/search_form_select.html"> Mass fingerprint search</A>  </TD></TR> <TR> <TD>  <A title="Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments" href="http://prospector.ucsf.edu/">Protein Prospector</A></TD></TR> <TR> <TD>  <A title="Allows the generation of a list of proteins close to a given pI and Mw, 
the identification of proteins by matching a short sequence tag of up to 6 amino acids against proteins in the SWISS-PROT/TrEMBL databases close to a given pI and Mw, 
the identification of proteins by their mass, if this mass has been determined by mass spectrometric techniques" href="http://ca.expasy.org/tools/tagident.html"> TagIdent</A></TD></TR> <TR> <TD>  <A href="http://bioweb.pasteur.fr/seqanal/interfaces/digest.html"> Digest</A></TD></TR> <TR> <TD>  <A href="http://www.scripps.edu/~cdputnam/protcalc.html"> Isoelectric point</A></TD></TR> <TR> <TD> </TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=institutes></A> <H4 align=center>Metabolic Pathways  Bioinformatics</H4></TD></TR> <TR> <TD>  <A title="WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models" href="http://wit.mcs.anl.gov/WIT2/">WIT - Interactive metabolic reconstruction</A></TD></TR> <TR> <TD>  <A title="Enzymes and Metabolic Pathways database, EMP, is a unique and most comprehensive electronic source of biochemical data, covering all aspects of enzymology and metabolism " href="http://emp.mcs.anl.gov/">EMP - Enzymes & Pathways database</A></TD></TR> <TR> <TD>  <A href="http://www.genome.ad.jp/">Genome Net - Ligand and Brenda </A></TD></TR> <TR> <TD>  <A title="Databases of Pathways of Reactions & Compounds in Living Cells" href="http://www-mbi3.kuicr.kyoto-u.ac.jp/~kihara/biolink/pathdb.html"> Metabolic Pathways Links</A></TD></TR> <TR> <TD>  <A href="http://www.biocarta.com/genes/index.asp"> BioCarta</A></TD></TR> <TR> <TD>  <A title="Comprehensive Enzyme Information System, Koeln" href="http://www.brenda.uni-koeln.de/">Brenda - Enzyme Database</A></TD></TR> <TR> <TD>  <A title="BioCyc collection of Pathway/Genome Databases and the Pathway Tools Software" href="http://biocyc.org/">BioCyc 6.5</A></TD></TR> <TR> <TD> </TD></TR> <TR> <TD> </TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top colSpan=2> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=5> <H4 align=center>Genomics Sequence Projects and Genome Informatics</H4></TD></TR> <TR bgColor=#ffffe0> <TD> <P align=center>     <STRONG>Plants</STRONG></P></TD> <TD> <P align=center><STRONG>Animals      </STRONG></P></TD> <TD> <P align=center> <STRONG>  Miscellanous</STRONG></P></TD></TR> <TR> <TD> <A title="Arabidopsis Genome Initiative" href="http://www.arabidopsis.org/"> Arabidopsis</A></TD> <TD> <A href="http://www.ornl.gov/hgmis/">Human </A>or <A title="Automatically annotated human genome" href="http://www.ensembl.org/">Ensembl</A></TD> <TD>  <A title="More than 150 eukaryotics sequence projects including more than 20 plant genome sequencing projects" href="http://wit.integratedgenomics.com/GOLD/eukaryagenomes.html"> Ongoing eukaryotic projects</A></TD></TR> <TR> <TD> <A title="The TIGR Rice Genome Project" href="http://www.tigr.org/tdb/e2k1/osa1/index.shtml"> Rice</A></TD> <TD> <A href="http://www.informatics.jax.org/"> Mouse</A></TD> <TD>  <A href="http://www.ncbi.nlm.nih.gov/LocusLink/"> LocusLink</A></TD></TR> <TR> <TD> <A href="http://www.cbc.umn.edu/ResearchProjects/Brassica/index.html"><EM> Brassica napus</EM></A></TD> <TD> <A href="http://zfish.wustl.edu/">Zebrafish</A></TD> <TD>  <A href="http://www.kazusa.or.jp/cyano/cyano.html"> Cyanobase</A></TD></TR> <TR> <TD> <A href="http://www.agron.missouri.edu/"> MaizeDB</A></TD> <TD> <A title="Berkeley Drosophila Genome Project" href="http://www.fruitfly.org/about/pubs/index.html"> Drosophila</A></TD> <TD>  <A title="Details of more than 200 projects collated by National Center Bioinformatics Information href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.html"> Microbial Genomes</A></TD></TR> <TR> <TD> <A title="Genomics of Wood Formation in Loblolly Pine" href="http://pinetree.ccgb.umn.edu/">Loblolly Pine</A></TD> <TD> <A title="Fugu Genomics Group at the HGMP-RC, part of its effort to map and sequence vertebrate genomes (Japanese puffer fish)" href="http://fugu.hgmp.mrc.ac.uk/">Fugu</A></TD> <TD>  <A title="Dictyostelium discoideum Genome Project" href="http://genome.imb-jena.de/dictyostelium/"> Dictyostelium</A></TD></TR> <TR> <TD></TD> <TD align=middle bgColor=#ffffe0><STRONG>Virus</STRONG></TD> <TD align=middle bgColor=#ffffe0><STRONG>Fungi</STRONG></TD></TR> <TR> <TD></TD> <TD> <A href="http://hiv-web.lanl.gov/">HIV</A></TD> <TD> <A title="Candida albicans information" href="http://alces.med.umn.edu/Candida.html"> Candida</A></TD></TR> <TR> <TD></TD> <TD></TD> <TD> <A title="The Schizosaccharomyces pombe Genome Sequencing Project" href="http://www.sanger.ac.uk/Projects/S_pombe/"> S.pombe</A></TD></TR> <TR> <TD colSpan=3> <TABLE cellSpacing=0 cellPadding=0 width="100%" border=0> <TBODY> <TR> <TD align=middle bgColor=#ffffe0><STRONG>Genome-wide bioinformatics analysis</STRONG></TD></TR> <TR> <TD> <A title="Bioinformatics mediated comparative analysis of completely sequenced microbial genomes" href="http://mbgd.genome.ad.jp/"> MBGD</A></TD></TR> <TR> <TD> <A title="Phylogenetic classification of orthologous proteins from complete genomes " href="http://www.ncbi.nlm.nih.gov/COG/"> COGs</A></TD></TR> <TR> <TD> <A title="Various whole genome bioinformatics comparisons" href="http://bioinfo.mbb.yale.edu/genome/">GeneCensus</A></TD></TR></TBODY></TABLE></TD> <TD></TD> <TD> </TD></TR></TBODY></TABLE></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> </TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=yeast></A> <H4 align=center>Yeast Bioinformatitcs</H4> <H4></H4></TD></TR> <TR> <TD>  <A href="http://genome-www.stanford.edu/Saccharomyces/">Saccharomyces Genome Database</A></TD></TR> <TR> <TD>  <A title="Comprehensive Yeast Genome Database" href="http://mips.gsf.de/proj/yeast/CYGD/db/index.html">CYGD</A></TD></TR> <TR> <TD>  <A href="http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl">Microarray expression data</A></TD></TR> </TBODY></TABLE><BR> </TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=2><A name=software></A> <H4 align=center>Free downloadable bioinformatics software</H4></TD></TR> <TR> <TD colSpan=2>  <A title="Great new toolbar (free) from MolBiol.Net which help you to navigate quickly to bioscience sites on the net, as well as having built in search engine capability" href="/toolbar/index.htm" >Bioscience Toolbar</A> </TD></TR> <TR> <TD colSpan=2>  <A title="Plasmid drawing utility - if you use this software please buy Kjeld Olesen a beer if you see him at a conference since this is beerware" href="http://www.acaclone.com/">pDRAW32</A></TD></TR> <TR> <TD colSpan=2>  <A title="Still available but no longer under development" href="http://www.crc.dk/dnatools/">DNA Tools</A></TD></TR> <TR> <TD>  <A href="http://www.mbio.ncsu.edu/BioEdit/bioedit.html">BioEDIT</A></TD></TR> <TR> <TD colSpan=2>  <A title="Biological sequence (ADN, protein) editor for GTK/Linux" href="http://www.pge.cnrs-gif.fr/bioinfo/gbioseq/index.php?lang=en">gBioSeq</A></TD></TR> <TR> <TD colSpan=2>  <A title="A list of Mac bioinformatics software from CellBiol.com" href="http://www.cellbiol.com/soft.htm">Mac Software</A></TD></TR><TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD colSpan=2>  <A target="ELISA software specialized for automated analysis and reporting - PhD students can apply for a free license" href="http://www.inside.net/easelisa">easELISA</A></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=institutes></A> <H4 align=center>bioinformatics Institutes</H4></TD></TR><TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD>  <A title="National Center for Biotechnology Information, the best bioinformatics resource on the internet" href="http://www.ncbi.nlm.nih.gov">NCBI</A> </TD></TR> <TR> <TD>  <A title="European bioinformatics Institue, the best bioinformatics resource on the internet" href="http://www.ebi.ac.uk">EBI</A></TD></TR> <TR> <TD>  <A title="Expert Protein Analysis System) proteomics server of the Swiss Institute of bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE" href="http://www.expasy.ch">ExPASy</A></TD></TR> <TR> <TD>  <A title="Genome Database" href="http://gdbwww.gdb.org/">GDB</A></TD></TR> <TR> <TD>  <A href="http://alces.med.umn.edu/">Alces</A></TD></TR> <TR> <TD>  <A href="http://www.ncgr.org/">NCGR</A></TD></TR> <TR> <TD>  <A title="Australian National Genomic Information Service" href="http://www.angis.org.au/new/index.html">ANGIS</A></TD></TR> <TR> <TD>  <A title="Max Planck Institute for Molecular Genetics" href="http://www.mpimg-berlin-dahlem.mpg.de/welcome.html">Max Planck</A></TD></TR> <TR> <TD>  <A title="U.K. national node of the European Molecular Biology Network" href="http://www.hgmp.mrc.ac.uk/About/SEQNET/">SeqNet</A></TD></TR></TBODY></TABLE></TD></TR><TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD> <H4 align=center>Vector databases</H4></TD></TR> <TR> <TD>  <A title="A collection of cloning vectors of Escherichia coli is kept at the Department of Microbial Genetics (NIG) as a resource for the biological research community" href="http://www.shigen.nig.ac.jp/cvector/cvector.html">Cloning Vector Collection</A></TD></TR></TBODY></TABLE><BR> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=institutes></A> <H4 align=center>Arabidopsis databases</H4></TD></TR> <TR> <TD>  <A title="Virtual library of plant microarray databases" href="http://www.univ-montp2.fr/%7Eplant_arrays/databases.html">Plant microarray databases</A> </TD></TR> <TR> <TD>  <A title="SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization" href="http://genome-www4.stanford.edu/MicroArray/SMD/">Stanford microarray database</A></TD></TR> <TR> <TD>  <A title="MIPS Arabidopsis thaliana database" href="http://mips.gsf.de/proj/thal/db/index.html">MIPS</A>' MATDB</TD></TR> <TR> <TD>  <A title="Arabidopsis Genome Resource" href="http://flora.life.nottingham.ac.uk/agr/">CropNet</A></TD></TR><TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD>  <TABLE cellSpacing=0 cellPadding=0 width="100%" border=0> <TBODY> <TR bgColor=#ffffe0> <TD align=middle><A name=tdna></A><STRONG>T-DNA Insertion Collections</STRONG></TD></TR> <TR> <TD>  <A title="Search against approximately 100,000 individual T-DNA mutagenized Arabidopsis plants (Columbia ecotype)" href="http://www.tmri.org/">Syngenta TMRI</A></TD></TR> <TR> <TD>  <A title="BLAST search against Arabidopsis sequence tagged inserts" href="http://nasc.nott.ac.uk/blast.html">NASC blast</A> or <A title="Submit sequences to be searched against NASC T-DNA insert collection sequenced inserts as soon as they are released, with notification of matches by email" href="http://nasc.nott.ac.uk/insertwatch/">Insertwatch (NASC)</A></TD></TR> <TR> <TD>  <A title="Blast search against T-DNA insertion sites of plants from the Alonso/Crosby/Ecker collections, available from the ABRC, courtesy of Salk Institute Genome Analysis Laboratory" href="http://signal.salk.edu/cgi-bin/tdnaexpress"> T-DNA Express</A> </TD></TR></TBODY></TABLE></TD></TR></TBODY></TABLE><BR> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 cols=4 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD><A name=institutes></A> <H4 align=center>Hidden markov models in bioinformatics </H4></TD></TR> <TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD>  <A title="Dynamic and heuristic sequence analysis tools on an FPGA bioinformatics supercomputer" href="http://decypher.stanford.edu/index_by_algo.htm">Decypher2</A></TD></TR> <TR> <TD> </TD></TR></TBODY></TABLE> <P></P></TD> <TD vAlign=top> <TABLE class=maintable borderColor=#fcfcef cellSpacing=2 borderColorDark=#fcfcef cellPadding=0 width="100%" bgColor=#fcfcef borderColorLight=#fcfcef border=0> <TBODY> <TR bgColor=#e6e6fa> <TD colSpan=2> <H4 align=center>Protein databases and domains </H4></TD></TR> <TR> <TD vAlign=top> <TABLE cellSpacing=0 cellPadding=0 width="100%" border=0> <TBODY> <TR> <TD align=middle bgColor=#ffffe0><STRONG>Protein Databases</STRONG></TD></TR> <TR> <TD>  <A title="ExPASy proteomic server - most of the protein sequences are inferred from the gene nucleotide sequence" href="http://www.expasy.ch/sprot/">Swiss-prot</A></TD></TR> <TR> <TD>  <A title="bioinformatics at Manchester" href="http://www.bioinf.man.ac.uk/dbbrowser/OWL">OWL</A></TD></TR> <TR> <TD align=middle bgColor=#ffffe0><STRONG>Protein Domains: Databases and Search Tools</STRONG></TD></TR> <TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD>  <A title="Protein Domain Database" href="http://www.toulouse.inra.fr/prodom.html">ProDom</A></TD></TR> <TR> <TD>  <A title="Search a library of profiles with a protein sequence " href="http://bmerc-www.bu.edu/bioinformatics/profile_request.html"> Protein Domain Profile Analysis </A></TD></TR> <TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD>  </TD></TR> <TR><TD><A HREF="http://www.bioinformatics.vg">Bioinformatics Portal</A></TD></TR> <TR> <TD></TD></TR></TBODY></TABLE></TD> <TD vAlign=top> </TD></TR></TBODY></TABLE><BR> <P> </P></TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR> <TR> <TD colSpan=2> </TD></TR> <TR> <TD> <HR> </TD> <TD> <HR> </TD></TR></TBODY></TABLE> <BR> <P align=center><BR><A title="Check It Out: The Best bioinformatics Sciences Bookshop Online!" target=_blank href="Books/index.htm">Go to Biology-Bookstore.Com for a high quality collection of biological sciences books!</A> </P> <P align=center>If you have any bioinformatics links to add to MolBiol.Net please contact <A href="mailto:bioinformatics@molbiol.net">bioinformatics@molbiol.net</A></P> <P> <TABLE cellSpacing=0 cellPadding=1 width="98%" align=center border=1> <TBODY> <TR borderColor=#0000ff bgColor=#ffffe0> <TD><A target="topp" href="chromeyellow/index.htm"><FONT face=Verdana color=#000000 size=1>Tools Menu</FONT></A></TD> <TD><A href="Books/Subjects/bioinformatics/index.htm"><FONT face=Verdana color=#000000 size=1>bioinformatics Books</FONT></A></TD> <TD><A href="Books/Subjects/bioinformatics/bioinformatics.htm"><FONT face=Verdana color=#000000 size=1>bioinformatics Booklist</FONT></A></TD> <TD><A href="what-is-bioinformatics.htm"><FONT face=Verdana color=#000000 size=1>What is bioinformatics</FONT></A></TD> <TD><A target=middleright href="contactf.htm"><FONT face=Verdana color=#000000 size=1>Contact bioinformatics.vg</FONT></A></TD> <TD><A target=middleright href="sgif.htm"><FONT face=Verdana color=#000000 size=1>Other useful bioinformatics sites</FONT></A></TD> <TD><A target="" href="Methods/PCRtutorialf.htm"><FONT face=Verdana color=#000000 size=1>PCR tutorial</FONT></A></TD></TR> <TR borderColor=#0000ff bgColor=#ffffe0> <TD><A href="main.htm"><FONT face=Verdana color=#000000 size=1>bioinformatics Links</FONT></A></TD> <TD><A href="Books/index.htm"><FONT face=Verdana color=#000000 size=1>Bioinformatics Bookstore</FONT></A><FONT face=Verdana size=1> </FONT></TD> <TD><A target=_blank href="http://groups.yahoo.com/group/molbiolnet"><FONT face=Verdana color=#000000 size=1>Discussion Group</FONT></A><A href="chromeyellow/index.htm"></A></TD> <TD><A href="tutorial-homolgous-genes.htm"><FONT face=Verdana color=#000000 size=1>bioinformatics Tutorial</FONT></A></TD> <TD><A target="topp" href="top_protocols.htm"><FONT face=Verdana color=#000000 size=1>Protocols</FONT></A></TD> <TD><A href="bookfinder.htm"><FONT face=Verdana color=#000000 size=1>Find a Book - 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