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Part 1: Molecular Biology Search and Analysis

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<a href="http://www.embl-heidelberg.de/srs/srsc?-info||ALI">3D-ALI</a> - Database relating Proteins Structures and Sequences (see <a href="gopher://s-crim1.dl.ac.uk/00/EMBnet%20Bioinformation%20Resource%20UK/Data%20%26%20Software/databases/3d_ali/3d_ali.doc">Documentation</a>) at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>   <a href="http://www.embl-heidelberg.de/aaa.html">AA Analysis </a> - Protein Identification in SwissProt and PIR using Amino Acid Composition at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>   <a href="http://expasy.hcuge.ch/ch2d/aacompi.html">AA CompIdent</a> - Protein Identification in SwissProt using Amino Acid Composition at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland   <a href="http://expasy.hcuge.ch/ch2d/aacsim.html">AA CompSim</a> - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland   <a href="http://chait-sgi.rockefeller.edu/cgi-bin/sequence/AA">AA Sequence Analysis</a> - Multiple Analysis of a Native or Modified Amino Acid Sequence at <a href="http://www.rockefeller.edu/ru.home.html">Rockefeller U.</a>   <a href="http://www.biochem.ucl.ac.uk/~martin/abs/seqtest.html">AbCheck</a> - Test an Antibody Sequence Against the Kabat Database at <a href="http://www.biochem.ucl.ac.uk/">U. College-London</a>, UK   <a href="http://genome.eerie.fr/fasta/align-query.html">ALIGN</a> - Optimal Global Alignment of Two Sequences with No Short-cuts at <a href="http://genome.eerie.fr/home.html">EERIE-Nimes</a>, France and <a href="http://speedy.mips.biochem.mpg.de/www/programs/align.html">Align</a> at <a href="http://speedy.mips.biochem.mpg.de/">MIPS</a>, Germany   <a href="http://cbrg.inf.ethz.ch/subsection3_1_1.html">AllAll</a> - Relationships in a Set of Related Peptides at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland   <a href="http://cbrg.inf.ethz.ch/subsection3_1_2.html">AllAllDB</a> - Search the All-Against-All Database of SwissProt at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland   <a href="http://geoff.biop.ox.ac.uk/servers/amas_server.html">AMAS</a> - Analysis of Protein Multiple Sequence Alignments at <a href="http://geoff.biop.ox.ac.uk/">U. Oxford</a>, UK   <a href="http://www.embl-heidelberg.de/argos/ASC.21/asc2.html">ASC</a> - Analytic Surface Calculation of PDB Protein Structures at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>   <a href="http://mips11.mips.biochem.mpg.de/www/programs/atlas_per.html">ATLAS</a> - Search DNA and Protein Sequence Databases at <a href="http://speedy.mips.biochem.mpg.de/">MIPS</a>, Germany   <a href="http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html">BCM Search Launcher</a> at <a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="></a> <a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="> </a><a href="http://dot.imgen.bcm.tmc.edu:9331/seq-search/protein-search.html">BEAUTY</a> - BLAST Enhanced Alignment Utility <a href="http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/beauty.html">(see Documentation)</a> at <a href="http://www.bcm.tmc.edu/">Baylor College of Medicine</a>   <a href="http://cammsg3.caos.kun.nl:8000/srs/srsc?-info+BERLIN">BERLIN</a> - RNA Databank of 5S rRNA and 5S rRNA Gene Sequences at <a href="http://cammsg3.caos.kun.nl:8000/">CAOS/CAMM</a>, The Netherlands   <a href="http://sgbcd.weizmann.ac.il/Bic/ExecAppl.html">BIOACCELERATOR</a> at <a href="http://bioinformatics.weizmann.ac.il:70/">Weizmann Institute of Science</a>, Israel   <a images="" alt="!New!" href="http://www.ocms.ox.ac.uk/~birney/cusi/biocusi.html%3E%3Cb%3EbioCUSI%3C/b%3E%3C/a%3E%3Cimg%20src=">- Multiple Access to Biological Servers at </a><a href="http://www.ocms.ox.ac.uk/">OCMS-Oxford</a>   <a href="ftp://pdb.pdb.bnl.gov/user_group/biological_units">Biological Units</a> - Expanded PDB Entries with Full Biological Units at <a href="http://suntid.bnl.gov:8080/bnl.html">Brookhaven National Laboratory</a>   <a href="http://www.ocms.ox.ac.uk/~birney/palette.html">Biologist's Search Palette</a> - Collection of Search Engines for Biological Databases at <a href="http://www.ocms.ox.ac.uk/">Oxford U.</a>, UK   <a href="http://www.ncbi.nlm.nih.gov/Recipon/bs_seq.html">BLAST</a> - Basic Local Alignment Research Tool at <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>, <a href="http://swarmer.stanford.edu/cgi-bin/blastq-form?options=simple">BLAST</a> (hiv, vector, etc) at <a href="http://motif.stanford.edu/">Stanford U.</a>, <a href="http://www.genome.ad.jp/SIT/BLAST.html">BLAST</a> at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan, <a href="http://genome.eerie.fr/blast/blast-query.html">BLAST</a> at <a href="http://genome.eerie.fr/home.html">EERIE-Nimes</a>, France, <a href="http://www.crihan.fr/www/blast.html">BLAST</a> at <a href="http://www.crihan.fr/">CRIHAN</a>, France <a href="http://dot.imgen.bcm.tmc.edu:9331/cgi-bin/seq-search/blast_form_local.pl">BLAST</a> (with Entrez and SRS Links) at <a href="http://gc.bcm.tmc.edu:8088/">Baylor College of Medicine</a> and <a href="http://ulrec3.unil.ch/software/EPFLBLAST_form.html">BLAST</a> at <a href="http://www.epfl.ch/">EPFL</a>, Switzerland   <a href="http://dot.imgen.bcm.tmc.edu:9331/seq-search/Option/blastpat.html">BLASTPAT</a> - BLAST-based Pattern Database Search (see <a href="http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/blastpat.html">Documentation</a>) at <a href="http://gc.bcm.tmc.edu:8088/">Baylor College of Medicine</a>   <a href="http://www.embl-heidelberg.de/searches/blitz_input.html">BLITZ</a> (see <a href="http://www.ebi.ac.uk/searches/blitz_doc.html">Documentation</a>) at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a> and <a href="http://www.ebi.ac.uk/searches/blitz_input.html">BLITZ</a> at <a href="http://www.ebi.ac.uk/">EBI</a>, UK   <a href="http://www.blocks.fhcrc.org/">BLOCKS</a> - Database of Highly Conserved Regions in Proteins  and <a href="gopher://klaatu.fhcrc.org/77/.indexes/.blocksindex/blocksindex">BLOCKS-WAIS</a>  at <a href="gopher://klaatu.fhcrc.org/">Fred Hutchinson Cancer Research Center</a>, <a href="http://www.embl-heidelberg.de/srs/srsc?-info||BLOCKS">BLOCKS</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a> and <a href="http://www.public.iastate.edu/~pedro/blocks_query.html">BLOCKS-Search</a> w/ search from <a href="http://www.cc.iastate.edu/welcome.html">Iowa State</a>   <a href="http://bimas.dcrt.nih.gov/sql/BMRBgate.html">BioMagResBank</a> - A Database of NMR-Derived Protein Structures at <a href="http://bimas.dcrt.nih.gov/">BIMAS-NIH</a>   <a href="http://genome.cs.unc.edu/online.html">BioSCAN</a> - Biological Sequence Comparative Analysis at <a href="http://genome.cs.unc.edu/">U. North Caroline</a>   <a href="http://ibm4.carb.nist.gov:4400/bmcd/bmcd.html">BMCD</a> - Biological Macromolecule Crystallization Database at <a href="http://ibm4.carb.nist.gov:4400/carb.html">CARB</a>   <a href="http://ulrec3.unil.ch/software/BOX_form.html">BOXSHADE</a> - Pretty Printing and Shading of Multiple-Sequence Alignments at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland   <a href="http://www.biochem.ucl.ac.uk/bsm/cath/CATHintro.html">CATH</a> - Protein Structure Classification at <a href="http://www.biochem.ucl.ac.uk/">UCL-London</a>, UK   <a href="http://ibc.wustl.edu/msa/clustal.cgi">CLUSTALW</a> - Multiply Sequence Alignments at <a href="http://ibc.wustl.edu/">IBC-Washington U.</a>   <a href="http://alces.med.umn.edu/cuse.html">Codon Usage</a> - Analysis of Different ORFs in a Gene Sequence at <a href="http://www.umn.edu/">U. Minnesota</a>   <a href="http://ulrec3.unil.ch/software/COILS_form.html">Coils</a> - Prediction of Coiled Coil Regions in Protein Sequences at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland   <a href="http://ben.vub.ac.be/srs/srsc?-info+CPGISLE">CpGIsle</a> - CpG Islands Database at <a href="http://ben.vub.ac.be/">BEN</a>, Belgium   <a href="http://cbrg.inf.ethz.ch/subsection3_1_7.html">Darwin</a> - Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland   <a href="http://www.ncbi.nlm.nih.gov/dbEST/index.html">dbEST</a> - Database of Expressed Sequence Tags at <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>   <a href="http://www.genome.ad.jp/dbget/dbget.html">DBGET</a> - Integrated Database Retrieval System (w/ <a href="http://www.genome.ad.jp/dbget/dbget.links.html">diagram links</a>) at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan   <a href="gopher://gopher.nig.ac.jp/7waissrc%3a/DDBJ_Gopher_WAIS/DNA_seq_index_search.src">DDBJ</a> - DNA Database of Japan at <a href="http://www.nig.ac.jp/">National Institute of Genetics</a>, Japan   <a href="http://alces.med.umn.edu/rawdot.html">Dot Plot</a> - Compare a DNA Sequence with Itself at <a href="http://www.umn.edu/">U. Minnesota</a>   <a href="http://www.nih.gov/molecular_modeling/drugbank.html">DrugBank</a> - Three-dimensional Drug Structure Databank at <a href="http://www.nih.gov/">NIH</a>   <a href="http://www.embl-heidelberg.de/srs/srsc?-info+DSSP">DSSP</a> - Database of Secondary Structure of Proteins from PDB (see <a href="http://www.sander.embl-heidelberg.de/dssp/descrip.html">Documentation</a>) at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>   <a href="http://www.gdb.org/Dan/proteins/ec-enzyme.html">EC Enzyme</a> at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a> and <a href="http://www.genome.ad.jp/htbin/show_ECtable">EC Number Table</a> at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan and <a href="http://specter.dcrt.nih.gov:8004/Enzymes/enzymes.html">GenoBase Enzyme Index</a> at <a href="http://www.nih.gov/">NIH</a>   <a href="http://susi.bio.uni-giessen.de/usr/local/www/html/ecdc.html">ECDC</a> - E. coli Database Collection at <a href="http://www.uni-giessen.de/">Uni-Gießen</a>, Germany   <a href="gopher://biox.embnet.unibas.ch:13021/77/.index/embl/index">EMBL</a> - Nucleotide Sequence Database and <a href="gopher://biox.embnet.unibas.ch:13021/77/.index/xembl/index">EMBL-New Entries</a> at <a href="http://www.ch.embnet.org/">EMBnet-Basel</a>   <a href="http://www.ebi.ac.uk/srs/srsc?-info||EMNEW">EMNEW</a> - Index of New EMBL Sequences at <a href="http://www.ebi.ac.uk/">EBI</a>, UK  <a href="http://specter.dcrt.nih.gov:8004/Compound/compound_toc_by_name.html">EMP Compound</a> and <a href="http://specter.dcrt.nih.gov:8004/Pathway/pathway_toc_by_name.html">EMP Pathways</a> - Selkov Enzyme and Metabolic Pathway (EMP) Database at <a href="http://www.nih.gov/">NIH</a>   <a href="http://www.mcs.anl.gov/home/towell/metabhome.html">EMP Metabolic Pathways</a> - Navigation in Metabolic Pathways from <a href="http://www.mcs.anl.gov/home/compbio/default.html">MCS-Computational Biology</a> at <a href="http://www.anl.gov/">Argonne National Laboratory</a>   <a href="http://www.ncbi.nlm.nih.gov/Search/Entrez/index.html">ENTREZ</a> - Protein and Nucleotide Database (see <a href="http://atlas.nlm.nih.gov:5700/WWW2/WWW2_paper2.html">Documentation</a>) at <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>   <a href="http://expasy.hcuge.ch/sprot/enzyme.html">ENZYME</a> - The Enzyme Data Bank at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland   <a href="http://www.biochem.ucl.ac.uk/bsm/enzymes/index.html">Enzyme Structures Database</a> - Structures of Enzymes Deposited in the PDB at <a href="http://www.biochem.ucl.ac.uk/">UCL-London</a>, UK

<a href="http://~~expasy~~www.~~hcuge~~embl-heidelberg.chde/~~ch2d~~srs/~~aacompi~~srsc?-id||781260221_129.186.~~html~~4.14||-info||EPD">~~AA CompIdent~~EPD</a> - ~~Protein Identification in SwissProt using Amino Acid Composition~~ Eucaryotic Promoter Database at <a href="http://~~expasy~~www.embl-heidelberg.de/">EMBL-Heidelberg</a>, Germany and <a href="http://www.genome.ad.jp/htbin/bfind_epd">EPD</a> at <a href="http://www.genome.~~hcuge~~ad.chjp/">~~ExPASy~~GenomeNet</a>, ~~Switzerland~~Japan

<a href="http://~~expasy~~bioslave.~~hcuge~~uio.chno:8001/~~ch2d~~srs/~~aacsim.html~~srsc?-info+EPO">~~AA CompSim~~EPO</a> - ~~Compare the Amino Acid Composition of~~ European Patent Office Nucleotide Database at <a href="http://www.no.embnet.org/">BiO/U. Oslo</a>, Norway  and <a href="gopher://gopher.csc.fi/7waissrc%3a/tiede/BioBox/bionic/.epo.src">EPO</a ~~SwissProt Entry with Other Entries~~ > at <a href="http://~~expasy~~www.~~hcuge~~csc.chfi/CSC_english.html">~~ExPASy~~CSC</a>, ~~Switzerland~~Finland

<a href="http://~~chait~~www.ebi.ac.uk/searches/fasta.html">FASTA</a> -~~sgi~~Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases (w/ updates) at <a href="http://www.ebi.~~rockefeller~~ac.uk/">EBI</a>, UK, <a href="http://swarmer.stanford.edu/cgi-bin/~~sequence~~fastaq-form?options=simple">FASTA</a> (Berlin, Vectorbank, etc) at <a href="http://motif.stanford.edu/AA">Stanford U.</a>, <a href="http://genome.eerie.fr/fasta/fasta-query.html">~~AA Sequence Analysis~~FASTA</a> at <a href="http://genome.eerie.fr/home.html">EERIE- ~~Multiple Analysis of~~ Nimes</a ~~Native or Modified Amino Acid Sequence at~~ >, France and <a href="http://www.~~rockefeller~~crihan.~~edu~~fr/www/~~ru.home~~fasta.html">~~Rockefeller U~~FASTA</a> at <a href="http://www.crihan.fr/">CRIHAN</a>, France

<a href="http://~~www~~dot.~~biochem~~imgen.~~ucl~~bcm.actmc.ukedu:9331/~~~martin~~seq-search/~~abs~~Options/~~seqtest~~fastpat.html">~~AbCheck~~FASTPAT</a> - ~~Test an Antibody Sequence Against the Kabat~~ FASTA-based Pattern Database at Search (see <a href="http://~~www~~dot.~~biochem~~imgen.~~ucl~~bcm.actmc.ukedu:9331/seq-search/Help/fastpat.html">UDocumentation</a>) at <a href="http://gc. bcm.tmc.edu:8088/">Baylor College~~-London~~of Medicine</a>~~, UK~~

<a href="http://~~genome~~morgan.~~eerie~~harvard.fredu/~~fasta/align-query.html~~">~~ALIGN~~FlyBase</a> - ~~Optimal Global Alignment of Two Sequences with No Short-cuts at <a href="http://genome.eerie.fr/home.html">EERIE-Nimes</a>, France~~ Genetic and Molecular Database for <~~a href="http://speedy.mips.biochem.mpg.de/www/programs/align.html"><strong~~em>~~Align~~Drosophila</~~strong></a~~em> at <a href="http://~~speedy.mips~~www.~~biochem~~harvard.~~mpg.de~~edu/">~~MIPS~~Harvard U.</a>~~, Germany~~

<a href="http://~~cbrg~~www.~~inf~~embl-heidelberg.~~ethz.ch~~de/srs/~~subsection3_1_1.html~~srsc?-info||FSSP">~~AllAll~~FSSP</a> - ~~Relationships in a Set~~ Database of Families of ~~Related Peptides~~ Structurally Similar Proteins derived from PDB at <a href="http://~~cbrg~~www.~~inf.ethz~~embl-heidelberg.chde/">~~ETH~~EMBL-~~Zürich~~Heidelberg</a>~~, Switzerland~~

<a href="http://~~cbrg~~www.~~inf~~abc.~~ethz.ch~~hu/~~subsection3_1_2~~blast.html">~~AllAllDB~~FTHOM</a> - ~~Search the All-Against-All Database of SwissProt~~ Compare Protein Domain Homology at <a href="http://~~cbrg~~www.~~inf~~abc.~~ethz.ch~~hu/">~~ETH-Zürich~~ABC</a>, ~~Switzerland~~Hungary

<a href="http://~~geoff~~gdbwww.~~biop~~gdb.~~ox.ac.uk~~org/~~servers/amas_server.html~~">~~AMAS~~GDB</a> - ~~Analysis of Protein Multiple Sequence Alignments~~ Human Genome Data Base at <a href="http://~~geoff~~www.~~biop~~gdb.oxorg/hopkins.~~ac.uk/~~html">~~U. Oxford~~Johns Hopkins</a>~~, UK~~

<a href="http://ncbi.nlm.nih.gov:2555/r_genbank2.html">GenBank Database</a> (+Updates) at <a href="http://www.~~embl-heidelberg~~ncbi.nlm.nih.degov/~~argos~~">NCBI</~~ASC~~a> and <a href="http://ibc.21wustl.edu/~~asc2~~wu_fetch.html">~~ASC~~GenBank-Fetch</a> ~~- Analytic Surface Calculation of PDB Protein Structures~~ at <a href="http://~~www~~ibc.~~embl-heidelberg~~wustl.deedu/">~~EMBL-Heidelberg~~Washington U.</a>

<a href="http://~~mips11~~dot.~~mips~~imgen.~~biochem~~bcm.~~mpg~~tmc.deedu:9331/~~www~~gene-finder/~~programs/atlas_per~~gf.html">~~ATLAS~~Gene Finder</a> - ~~Search~~ Predict Gene Structure, Internal Exons and Splicing Sites in DNA and ~~Protein Sequence Databases~~ Exon-Exon Junstion in cDNA at <a images="" alt="(W3)" href="http://~~speedy~~www.~~mips~~bcm.~~biochem~~tmc.~~mpg.de~~edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src=">~~MIPS~~</a>~~, Germany ~~

~~ <a href="http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html">BCM Search Launcher</a> at~~ <a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="> </a><a href="http://cbil.humgen.upenn.edu/~sdong/genlang_home.html">GenLang</a> - Find Genes and Other Higher-Order Features in Nucleotide Sequences at <a href="http://cbil.humgen.upenn.edu/">CBIL-U. Pennsylvania</a>

~~<a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src=">~~ ~~</a><a href="http://dot.imgen.bcm.tmc.edu:9331/seq-search/protein-search.html">BEAUTY</a> - BLAST Enhanced Alignment Utility~~ <a href="http://~~dot.imgen~~specter.~~bcm~~dcrt.~~tmc~~nih.~~edu~~gov:~~9331/seq-search/Help~~8004/~~beauty.html~~">~~(see Documentation)~~GenoBase</a> at <a href="http://www.~~bcm.tmc~~nih.~~edu~~gov/">~~Baylor College of Medicine~~NIH</a>

<a href="http://~~cammsg3~~genome.~~caos~~eerie.~~kun~~fr/Genome-DBS.nlhtml">Genome Databases</a> and <a href="http:~~8000~~/~~srs~~/~~srsc?-info+BERLIN~~genome.eerie.fr/Genome_Centre.html">~~BERLIN~~Genome Centers</a> - ~~RNA Databank of 5S rRNA and 5S rRNA Gene Sequences~~ World Wide Links at <a href="http://~~cammsg3.caos~~genome.~~kun~~eerie.~~nl:8000~~fr/">~~CAOS/CAMM~~EERIE-Nimes</a>, ~~The Netherlands~~France

<a href="http://~~sgbcd~~www.~~weizmann~~ri.bbsrc.ac.iluk/~~Bic~~genome_workstation/~~ExecAppl~~workstation.html">~~BIOACCELERATOR~~Genome Workstation</a> - Genome Related Links at <a href="http://~~bioinformatics~~www.~~weizmann~~ri.bbsrc.ac.~~il:70~~uk/">~~Weizmann~~ Roslin Institute ~~of Science~~</a>, ~~Israel~~UK

<a ~~images="" alt="!New!"~~ href="http://~~www~~biotech.~~ocms~~chem.oxindiana.~~ac.uk~~edu/~~~birney~~WebChris/~~cusi/biocusi~~maps.html~~%3E%3Cb%3EbioCUSI%3C~~">Genomic Maps</~~b%3E%3C~~strong></a~~%3E%3Cimg%20src="~~>- ~~Multiple Access~~ Links to ~~Biological Servers~~ Genome Specific Resources at ~~</a>~~<a href="http://~~www.ocms~~biotech.oxchem.acindiana.ukedu/">~~OCMS~~Biotech-~~Oxford~~Indiana</a>

<a href="~~ftp~~http://~~pdb~~www.~~pdb~~gdb.~~bnl.gov~~org/Dan/~~user_group~~gq/~~biological_units~~gq.form.html">~~Biological Units~~GenQuest</a> - ~~Expanded PDB Entries~~ Search Against Protein Databases with ~~Full Biological Units~~ the Q server at <a href="http://~~suntid~~www.~~bnl~~gdb.~~gov:8080~~org/~~bnl~~hopkins.html">~~Brookhaven National Laboratory~~Johns Hopkins</a>

<a href="http://~~www~~avalon.~~ocms~~epm.oxornl.acgov/Grail-bin/EmptyGrailForm">Grail</a> - Analysis of the Protein Coding Potential of a DNA Sequence (see <a href="ftp://arthur.epm.ukornl.gov/~~~birney~~pub/~~palette~~xgrail/Manual.~~html~~grail-genquest.July94">~~Biologist's Search Palette~~Documentation</a> ~~- Collection of Search Engines for Biological Databases~~ ) at <a href="http://~~www.ocms~~avalon.oxepm.acornl.ukgov/">~~Oxford U.~~ORNL</a>~~, UK~~

<a href="http://www.~~ncbi~~ncgr.nlm.nih.gov/Recipon/bs_seq.html">BLAST</a> - Basic Local Alignment Research Tool at <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>, <a href="http://swarmer.stanford.edu/cgi-bin/blastq-form?options=simple">BLAST</a> (hiv, vector, etc) at <a href="http://motif.stanford.edu/">Stanford U.</a>, <a href="http://www.genome.ad.jp/SIT/BLAST.html">BLAST</a> at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan, <a href="http://genome.eerie.frorg/~~blast~~gsdb/~~blast-query.html~~">~~BLAST~~GSDB</a> ~~at <a href="http://genome.eerie.fr/home.html">EERIE~~-~~Nimes</a>, France, <a href="http://www.crihan.fr/www/blast.html">BLAST</a>~~ Genome Sequence Database at <a href="http://www.~~crihan~~ncgr.~~fr/">CRIHAN</a>, France <a href="http:~~org/ncgr/dot.imgen.bcm.tmc.edu:9331/cgi-bin/seq-search/blast_form_local.pl">BLAST</a> (with Entrez and SRS Links) at <a href="http://gc.bcm.tmc.edu:8088/">Baylor College of Medicine</a> and <a href="http://ulrec3.unil.ch/software/EPFLBLAST_formncgr.html">~~BLAST</a> at <a href="http://www.epfl.ch/">EPFL~~NCGR</a>~~, Switzerland~~

<a href="http://~~dot~~expasy.~~imgen~~hcuge.~~bcm.tmc.edu:9331~~ch/www/~~seq~~guess-~~search/Option/blastpat~~prot.html">~~BLASTPAT~~GuessProt</a> - ~~BLAST-based Pattern Database Search (see <a href="http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/blastpat.html">Documentation</a>)~~ Selects SwissProt proteins given pI and Mw at <a href="http://gcexpasy.~~bcm~~hcuge.~~tmc.edu:8088~~ch/">~~Baylor College of Medicine~~ExPASy</a>, Switzerland

<a href="http://~~www~~ibc.~~embl-heidelberg.de/searches/blitz_input.html">BLITZ</a> (see <a href="http://www~~wustl.~~ebi.ac.uk~~edu/~~searches~~hhs/~~blitz_doc.html~~">~~Documentation~~HHS</a>~~) at <a href="http://www.embl-heidelberg.de/">EMBL~~-~~Heidelberg</a>~~ SwissProt and PDB Systematic Sequence Classification Database at <a href="http://~~www~~ibc.~~ebi~~wustl.~~ac.uk~~edu/~~searches/blitz_input.html~~">~~BLITZ</a> at <a href="http://www.ebi~~Washington U.~~ac.uk/">EBI~~</a>~~, UK~~

<a href="http://~~www~~cammsg3.~~blocks~~caos.~~fhcrc~~kun.org/">BLOCKS</a> - Database of Highly Conserved Regions in Proteins  and <a href="gopher://klaatu.fhcrc.org/77/.indexes/.blocksindex/blocksindex">BLOCKS-WAIS</a>  at <a href="gopher://klaatu.fhcrc.org/">Fred Hutchinson Cancer Research Center</a>, <a href="httpnl:~~//www.embl-heidelberg.de~~8000/srs/srsc?-info~~||BLOCKS~~+HOVERGEN">~~BLOCKS~~HOVERGEN</a> - Database of Homologous Vertebrate Genes at <a href="http://~~www~~cammsg3.caos.~~embl-heidelberg~~kun.~~de/">EMBL-Heidelberg</a> and <a href="http~~nl:8000/~~/www.public.iastate.edu/~pedro/blocks_query.html~~">~~BLOCKS-Search<~~CAOS/~~strong></a> w/ search from <a href="http://www.cc.iastate.edu/welcome.html">Iowa State~~CAMM</a>, The Netherlands

<a href="http://~~bimas~~speedy.~~dcrt~~mips.~~nih~~biochem.~~gov~~mpg.de/~~sql~~www/~~BMRBgate~~programs/hpt_persistent.html">~~BioMagResBank~~HPT</a> - A Protein Sequence Pattern Recognition in the PIR Database ~~of NMR~~and <a href="http://speedy.mips.biochem.mpg.de/www/programs/hpt_homol.html">HPT-~~Derived Protein Structures~~ Homology</a> at <a href="http://~~bimas~~speedy.mips.~~dcrt~~biochem.~~nih~~mpg.~~gov~~de/">~~BIMAS-NIH~~MIPS</a>, Germany

<a href="http://~~genome~~www.csembl-heidelberg.~~unc.edu~~de/srs/~~online.html~~srsc?-info||HSSP">~~BioSCAN~~HSSP</a> - ~~Biological Sequence Comparative Analysis~~ Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at <a href="http://~~genome~~www.csembl-heidelberg.~~unc.edu~~de/">~~U. North Caroline~~EMBL-Heidelberg</a>

<a href="~~http~~gopher://~~ibm4.carb~~gopher.~~nist~~gdb.~~gov:4400~~org/~~bmcd~~77/~~bmcd~~.~~html~~INDEX/kabat">~~BMCD~~Kabat </a> - ~~Biological Macromolecule Crystallization~~ Database of Proteins of Immunological Interest at <a href="http://~~ibm4~~www.~~carb~~gdb.~~nist.gov:4400~~org/~~carb~~hopkins.html">~~CARB~~Johns Hopkins</a>

<a href="http://~~ulrec3~~www.~~unil~~prosci.chuci.edu/~~software~~kinemages/~~BOX_form~~KinemageIndex.html">~~BOXSHADE~~Kinemage-Index</a> - ~~Pretty Printing and Shading of Multiple-Sequence Alignments~~ "Kinetical Images" by Protein Type at <a href="http://~~ulrec3~~www.prosci.~~unil~~uci.chedu/">~~ISREC~~Protein Science</a>~~, Switzerland~~

<a href="http://~~www~~ibc.~~biochem~~wustl.~~ucl.ac.uk/bsm~~edu/~~cath~~klotho/~~CATHintro.html~~">~~CATH~~Klotho</a> - ~~Protein Structure Classification~~ Biochemical Compounds Declarative Database at <a href="http://~~www.biochem.ucl~~ibc.acwustl.ukedu/">~~UCL-London~~Washington U.</a>~~, UK~~

<a href="http://~~ibc~~genome.~~wustl~~eerie.~~edu~~fr/~~msa~~fasta/~~clustal~~lalign-query.~~cgi~~html">~~CLUSTALW~~LALIGN</a> - ~~Multiply Sequence~~ Calculates the N-Best Local Alignments Between Two Sequences at <a href="http://~~ibc~~genome.~~wustl~~eerie.~~edu~~fr/home.html">~~IBC~~EERIE-~~Washington U.~~Nimes</a>, France

<a href="http://~~alces~~genome.~~med~~eerie.~~umn.edu~~fr/fasta/~~cuse~~lfasta-query.html">~~Codon Usage~~LFASTA</a> - ~~Analysis of Different ORFs in a Gene Sequence~~ Local Similarity Searches Between Two Sequences Showing Local Alignments at <a href="http://~~www~~genome.~~umn~~eerie.~~edu~~fr/home.html">~~U. Minnesota~~EERIE-Nimes</a>, France

<a href="http://~~ulrec3~~www.~~unil~~genome.chad.jp/~~software~~htbin/~~COILS_form.html~~bfind_ligand">~~Coils~~LIGAND</a> - ~~Prediction of Coiled Coil Regions in Protein Sequences~~ Ligand Chemical Database for Enzyme Reactions at <a href="http://~~ulrec3~~www.genome.~~unil~~ad.chjp/">~~ISREC~~GenomeNet</a>, ~~Switzerland~~Japan

<a href="gopher://gopher.nih.gov/77/gopherlib/indices/limb/index">LiMB</a> - Listing of Molecular Biology Databases at <a href="http://~~ben~~www.nih.~~vub~~gov/">NIH</a>  and <a href="http://www.acembl-heidelberg.bede/srs/srsc?-id||777855676_129.186.4.14||-info~~+CPGISLE~~||LIMB">~~CpGIsle~~LiMB</a> ~~- CpG Islands Database~~ at <a href="http://~~ben~~www.~~vub~~embl-heidelberg.~~ac.be~~de/">~~BEN~~EMBL-Heidelberg</a>~~, Belgium~~

<a href="http://cbrg.inf.ethz.ch/~~subsection3_1_7~~subsection3_1_3.html">~~Darwin~~MassSearch</a> - ~~Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences~~ Search SwissProt or EMBL Databases by Protein Mass After Digestion at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland

<a href="http://~~www~~cgsc.~~ncbi~~biology.~~nlm~~yale.~~nih.gov/dbEST~~edu/~~index~~metab.html">~~dbEST~~Metabolic Database</a> - ~~Database of Expressed Sequence Tags~~ Metabolic Reactions and Pathways at <a href="http://~~www~~cgsc.~~ncbi~~biology.~~nlm~~yale.~~nih~~edu/">CGSC-Yale U.~~gov~~</a> and <a href="http://moulon.inra.fr/cgi-bin/nph-acedb3.1/acedb/metabolisme?find+Reaction_or_pathway%3By+14+69">~~NCBI~~Metabolic Database</a> at <a href="http://moulon.inra.fr/">INRA-Moulon</a>, France

<a href="http://www.~~genome~~informatics.adjax.jporg/~~dbget/dbget~~mgd.html">~~DBGET~~MGD</a> - ~~Integrated~~ Mouse Genome Database ~~Retrieval System (w/ <a href="http://www.genome.ad.jp/dbget/dbget.links.html">diagram links</a>)~~ at <a href="http://www.~~genome~~informatics.adjax.jporg/">~~GenomeNet~~Jackson Laboratory</a>~~, Japan~~

<a href="gopher://~~gopher~~wehil.~~nig~~wehi.acedu.jpau/~~7waissrc%3a~~11/~~DDBJ_Gopher_WAIS/DNA_seq_index_search~~MHCPEP.~~src~~DB">~~DDBJ~~MHCPEP</a> - ~~DNA~~ Database of ~~Japan~~ Major Histocompatibility Complex (MHC) Binding Peptides at <a href="http://www.~~nig~~wehi.acedu.jpau/">~~National Institute of Genetics~~WEHI-Melbourne</a>, ~~Japan~~Australia

<a href="http://~~alces~~speedy.~~med~~mips.~~umn~~biochem.~~edu~~mpg.de/~~rawdot~~www/programs/hpt_persistent.html">~~Dot Plot~~MIPS-Alert</a> - ~~Compare a DNA~~ Automated Sequence ~~with Itself~~ Information Queries at <a href="http://~~www~~speedy.mips.biochem.~~umn~~mpg.~~edu~~de/">~~U. Minnesota~~MIPS</a>, Germany

<a href="http://www.nih.gov/~~molecular_modeling~~htbin/~~drugbank.html~~pdb">~~DrugBank~~Molecules R US</a> - ~~Three-dimensional Drug Structure Databank~~ Interactive Text and Images of PDB Files at <a href="http://www.nih.gov/">NIH</a>

<a href="http://www.embl-heidelberg.de/srs/srsc?-id||777855676_129.186.4.14||-info~~+DSSP~~||MOLPROBE">~~DSSP~~MPBD</a> - ~~Database of Secondary Structure of Proteins from PDB (see~~ Molecular Probe Data Base at <a href="http://www~~.sander~~.embl-heidelberg.de/~~dssp~~">EMBL-Heidelberg</a>  and <a href="gopher://~~descrip~~gopher.~~html~~slu.se/7waissrc%3a/wais-dbs/Biology/Oligos">~~Documentation~~MPDB</a>) at <a href="~~http~~gopher://~~www~~gopher.~~embl-heidelberg~~slu.dese/">~~EMBL-Heidelberg~~U. Agricultural Sciences</a>, Sweden

<a href="http://~~www~~cuhhca.~~gdb~~hhmi.~~org/Dan/proteins/ec-enzyme~~columbia.~~html">EC Enzyme<~~edu/~~strong><~~moose/~~a> at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a> and <a href="http://www.genome.ad.jp/htbin/show_ECtable~~">~~EC Number Table~~MOOSE</a> - Macromolecular Object Oriented Search Engine to Extract PDB Contained Information at <a href="http://~~www.genome.ad.jp/">GenomeNet</a>, Japan and <a href="http://specter~~cuhhca.~~dcrt~~hhmi.~~nih~~columbia.~~gov:8004/Enzymes~~edu/~~enzymes.html~~">~~GenoBase Enzyme Index</a> at <a href="http://www.nih~~Columbia U.~~gov/">NIH~~</a>

<a href="http://~~susi~~ibc.~~bio~~wustl.~~uni-giessen.de/usr/local/www/html~~edu/~~ecdc~~msa.html">~~ECDC~~MSA</a> - ~~E. coli Database Collection~~ Multiple Sequence Alignment at <a href="http://~~www~~ibc.~~uni-giessen~~wustl.deedu/">~~Uni-Gießen~~Washington U.</a>~~, Germany~~

<a href="~~gopher~~http://~~biox~~www.~~embnet~~genome.~~unibas~~ad.~~ch:13021~~jp/77SIT/MOTIF.~~index/embl/index~~html">~~EMBL~~MOTIF</a> - ~~Nucleotide Sequence Database and~~ Search Patterns in Protein Sequences at <a href="~~gopher~~http://~~biox~~www.~~embnet~~genome.~~unibas~~ad.chjp/">GenomeNet</a>, Japan <a href="http:~~13021~~/77/www.public.~~index~~iastate.edu/~~xembl~~~pedro/~~index~~motif_query.html">~~EMBL-New Entries~~Motif</a> at <a href="http://www.chgenome.ad.jp/">GenomeNet</a>, Japan w/ search from <a href="http://www.cc.~~embnet~~iastate.~~org~~edu/welcome.html">~~EMBnet-Basel~~Iowa State</a>

<a href="http://~~www~~dot.imgen.~~ebi~~bcm.actmc.ukedu:9331/~~srs~~multi-align/~~srsc?~~multi-~~info||EMNEW~~align.html">~~EMNEW~~Multiple Sequence Alignments</a> - ~~Index of New EMBL Sequences~~ CLUSTAL-W, MAP, and PIMA alignments at <a href="http://www.~~ebi~~bcm.actmc.ukedu/">~~EBI~~Baylor College of Medicine</a>~~, UK~~

<a href="http://~~specter~~ndbserver.~~dcrt~~rutgers.~~nih.gov:8004/Compound/compound_toc_by_name.html">EMP Compound</a> and <a href="http:/~~edu/~~specter.dcrt.nih.gov:8004/Pathway/pathway_toc_by_name.html~~">~~EMP Pathways~~NDB</a> - ~~Selkov Enzyme and Metabolic Pathway (EMP)~~ Nucleic Acid Database at ~~<a href="http://www~~Rutgers U.~~nih.gov/">NIH</a>~~

<a href="http://www.~~mcs~~cmpharm.~~anl~~ucsf.~~gov~~edu/~~home~~~nomi/~~towell/metabhome~~nnpredict.html">~~EMP Metabolic Pathways~~nnPredict</a> - ~~Navigation in Metabolic Pathways from~~ Predict Protein Secondary Structure at <a href="http://wormworld.ucsf.edu/">UCSF</a> and <a href="http://www.~~mcs~~public.~~anl~~iastate.~~gov~~edu/~~home~~~pedro/~~compbio/default~~nnpredict_query.html">~~MCS-Computational Biology~~nnPredict</a> at w/ search from <a href="http://www.~~anl~~cc.iastate.~~gov~~edu/welcome.html">~~Argonne National Laboratory~~Iowa State</a>

<a href="http://www.~~ncbi~~gdb.~~nlm.nih.gov~~org/~~Search~~Dan/~~Entrez~~proteins/~~index~~nrl3d.html">~~ENTREZ~~NRL_3D</a> - ~~Protein and Nucleotide~~ Sequence/Structure Database ~~(see~~ derived from PDB at <a href="http://~~atlas~~www.~~nlm~~gdb.~~nih~~org/hopkins.~~gov~~html">Johns Hopkins</a> and <a href="http:~~5700~~/~~WWW2~~/~~WWW2_paper2~~www.embl-heidelberg.~~html~~de/srs/srsc?-info||NRL3D">~~Documentation~~NRL_3D</a>) at <a href="http://www.~~ncbi.nlm.nih~~embl-heidelberg.~~gov~~de/">~~NCBI~~EMBL-Heidelberg</a>

<a href="http://~~expasy~~ddbjs4h.~~hcuge~~genes.~~ch/sprot~~nig.ac.jp/~~enzyme.html~~">~~ENZYME~~NRSub</a> - ~~The Enzyme Data Bank~~ A Non-Redundant DNA Sequence Database for Bacillus subtilis at <a href="http://~~expasy~~www.nig.~~hcuge~~ac.chjp/">~~ExPASy~~National Institute of Genetics</a>, ~~Switzerland~~Japan

<a href="http://cbrg.inf.ethz.ch/subsection3_1_4.html">NuclPepSearch</a> - Search SwissProt for a Nucletide Sequence at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland

<a href="http://chait-sgi.rockefeller.edu/">NYC-MASS</a> - Protein Mass Spectrometry Database at <a href="http://www.rockefeller.edu/ru.home.html">Rockefeller U.</a>

<a href="http://www.embl-heidelberg.de/obstruct/obs_form.html">OBSTRUCT</a> - Correlate Sequence Subsets of PDB Protein Structures at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://gdbwww.gdb.org/omimdoc/omimtop.html">OMIM</a> - Online Mendelian Inheritance in Man at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a>

<a href="gopher://megasun.bch.umontreal.ca/11/Organelles/Genomes">Organelle Genome</a>  - A Sequence Database at <a href="gopher://megasun.bch.umontreal.ca/">U. Montreal</a>

<a href="http://biotech.chem.indiana.edu/lib/orgstrain.html">Organisms and Strains</a> - Links to Databases Specific to Organism and Cell Collections at <a href="http://biotech.chem.indiana.edu/">Biotech-Indiana</a>

<a href="http://www.gdb.org/Dan/proteins/owl.html">OWL</a> - Non-Redundant Protein Sequence Database (Updated Daily) at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a> and <a href="http://www.biochem.ucl.ac.uk/~attwood/OWL/OWL.html">OWL</a> at <a href="http://www.biochem.ucl.ac.uk/">UCL-London</a>, UK

<a href="http://www.mcs.anl.gov/home/papka/ROSS/patscan.html">PatScan</a> - Look for Pattern Matches in DNA or Protein Sequences at <a href="http://www.mcs.anl.gov/">Argonne National Laboratory</a>

<a href="http://ulrec3.unil.ch/software/PATFND_form.html">PatternFind</a> - Search the SwissProt and Genpept Protein Sequence Databases with a <a href="http://expasy.hcuge.ch/txt/profile.txt">PROSITE-formatted</a> Pattern at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland

<a href="http://www-pdd.ncifcrf.gov/PDD/GEN-docs/indexGEN.html">PDD</a> - Protein Disease Database at <a href="http://www-pdd.ncifcrf.gov/">NIMH-NCI</a>

<a href="http://www.pdb.bnl.gov:4148/cgi-bin/browse">PDB-Browser</a>, <a href="gopher://pdb.pdb.bnl.gov/77/xfullindex/full">PDB-Index</a> and <a href="gopher://pdb.pdb.bnl.gov/77/xstatusindex/status">PDB-Pending</a> - <a href="http://www.pdb.bnl.gov/">Protein Data Bank</a> Structures at <a href="http://suntid.bnl.gov:8080/bnl.html">Brookhaven National Laboratory</a>, <a href="http://www.genome.ad.jp/htbin/bfind_pdb">PDB</a> at <a href="http://www.genome.ad.jp/">GenomeNet</a> Japan, <a href="http://www.ibf.unige.it/7/sci/.PDB/pdbsearch">PDB</a> at <a href="http://www.ibf.unige.it/">U. Genova</a>, Italy, <a href="http://www.ucmb.ulb.ac.be/pdb_seq_rel_jan94">PDB-List</a> and <a href="http://www.ucmb.ulb.ac.be/pdb_annot_jan94">PDB-Annotated</a> at <a href="http://www.ucmb.ulb.ac.be/index.html">Brussels Free U.</a>, Belgium and <a href="http://www.sander.embl-heidelberg.de/pdbsel/explanation.html">PDB-Select</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www.nih.gov/molecular_modeling/pdb_at_a_glance.html">PDB At A Glance</a> - Hierarchic Access to PDB Files at <a href="http://www.nih.gov/">NIH</a>

<a href="http://www.embl-heidelberg.de/srs/srsc?-id||781260221_129.186.4.14||-info||PDBFINDER">PDBFINDER</a> - A Database Containing PDB, DSSP and HSSP Information (see <a href="http://www.sander.embl-heidelberg.de/pdbfinder/overview.html">Documentation</a>) at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www.genome.ad.jp/htbin/bfind_pdbstr">PDBSTR</a> - Re-organized Protein Data Bank at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan

<a href="http://cbrg.inf.ethz.ch/subsection3_1_5.html">PepPepSearch</a> - Search SwissProt for a Peptide Sequence at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland

<a href="http://lenti.med.umn.edu/~shoop/sample.html">Plant EST Analysis</a> - Similarity Analysis of Different Plant cDNA/EST Sequences at <a href="http://lenti.med.umn.edu/">U. Minnesota</a>

<a href="http://www.public.iastate.edu/~pedro/pprotein_query.html">PHD</a> - Predict Protein Secondary Structure at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a> w/ search from <a href="http://www.cc.iastate.edu/welcome.html">Iowa State</a>

<a href="http://www.pasteur.fr/sas/phy/boot-sub.html">PHILIP-Bootstrapping Analysis</a> - Divergence Between Protein or Nucleotide Sequences at <a href="http://www.pasteur.fr/">Institut Pasteur</a>, France

<a href="http://genome.eerie.fr/gcg/phospepsort-query.html">Phospepsort</a> - Digest Phosphorylated Peptide Sequences at <a href="http://genome.eerie.fr/home.html">EERIE-Nimes</a>, France

<a href="http://expasy.hcuge.ch/ch2d/pi_tool.html">pI/Mw</a> - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland

<a href="http://www.gdb.org/Dan/proteins/pir.html">PIR</a> - Protein Identification Resource Database at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a>

<a href="http://www.embl-heidelberg.de/srs/srsc?-info||PIRALN">PIRALN</a> - Database of Sequence Alignments based on PIR at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www.genome.ad.jp/htbin/bfind_pmd">PMD</a> - Protein Mutant Database at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan and <a href="http://www.embl-heidelberg.de/srs/srsc?-info||PMD">PMD</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://alces.med.umn.edu/pmotif.html">PMOTIF</a> - Search Protein Motifs in Gene Sequence at <a href="http://www.umn.edu/">U. Minnesota</a>

<a href="http://www.biophys.uni-duesseldorf.de/service/polandform.html">Poland</a> - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at <a href="http://www.biophys.uni-duesseldorf.de/">Uni-Düsseldorf</a>, Germany

<a href="http://www.embl-heidelberg.de/predictprotein/predictprotein.html">PredictProtein</a> - Predict Protein Secondary Structure at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www.genome.ad.jp/htbin/bfind_prf">PRF</a> - Protein Research Foundation Sequence Database at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan

<a href="http://www-genome.wi.mit.edu/cgi-bin/primer2.2/primer_front">Primer</a> - Select PCR Primers in a Gene Sequence at <a href="http://www-genome.wi.mit.edu/">WICGR-MIT</a> and <a href="http://alces.med.umn.edu/rawprimer.html">Primer</a> at <a href="http://www.umn.edu/">U. Minnesota</a>

<a href="http://www.biochem.ucl.ac.uk/~attwood/PRINTS/PRINTS.html">PRINTS</a> - Protein Motif Fingerprints Database (see <a href="file://gopher.embl-heidelberg.de/pub/databases/prints/prints.doc">Documentation</a>) and <a href="http://www.biochem.ucl.ac.uk/~attwood/ALIGN/ALIGN.html">PRINTS-ALIGN</a> at <a href="http://www.biochem.ucl.ac.uk/">UCL-London</a>, UK and <a href="http://www.ch.embnet.org/srs/srsc?-info+PRINTS">PRINTS</a> at <a href="http://www.ch.embnet.org/">EMBnet-Basel</a>, Switzerland

<a href="http://protein.toulouse.inra.fr/prodom.html">ProDom</a> - A Protein Domain Database and <a href="http://protein.toulouse.inra.fr/prodom/blast_form.html">ProDom-Search</a> at <a href="http://www.jouy.inra.fr/infoservices-INRA/infoservices_donnees.html">INRA-Toulouse</a>, France, <a href="http://www.sanger.ac.uk/~esr/prodom.html">ProDom</a> and <a href="http://www.sanger.ac.uk/~esr/prodom-blast.html">ProDom-Search</a> at <a href="http://www.sanger.ac.uk/">Sanger Centre</a>, UK and <a href="http://www.embl-heidelberg.de/srs/srsc?-id||777855676_129.186.4.14||-info||PRODOM">ProDom</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://ulrec3.unil.ch/software/PRFSCAN_form.html">ProfileScan </a> - Search a Sequence Against a Library of Profiles at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland

<a href="gopher://bmerc-gopher.bu.edu/11/Databases/prolink">ProLink</a> - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information at <a href="http://bmerc-www.bu.edu/">BMERC</a>

<a href="http://www.embl-heidelberg.de/prs.page">PROPSEARCH</a> - Protein Sequence Search for Structural Homology Based on Aminoacid Properties at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://expasy.hcuge.ch/sprot/prosite.html">PROSITE</a> - Protein Sites and Patterns Database at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland, <a href="http://ulrec3.unil.ch/software/PSTSCAN_form.html">PrositeScan</a> at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland and <a href="http://www.ebi.ac.uk/searches/prosite_input.html">PROSITE-Search</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="file://ftp.embl-heidelberg.de/pub/databases/protein_extras">Protein-Extras</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www.public.iastate.edu/~pedro/p_families.html">Protein Families</a> - Links to Information on Different Protein Families at <a href="http://www.cc.iastate.edu/">Iowa State</a>

<a href="http://chait-sgi.rockefeller.edu/cgi-bin/prot-id/1/1">Prot-ID</a> - Identify a Protein from Masses of Enzymatic Digestion Peptide Fragments at <a href="http://chait-sgi.rockefeller.edu/">Rockefeller U.</a>

<a href="file://cb-iris.stanford.edu/pub/ProteinMovements/ProtMotDB.main.html">Protein Motions</a>  - DataBase of Protein Movements at <a href="http://hyper.stanford.edu/">Stanford U.</a>

<a href="http://bmerc-www.bu.edu/psa/">PSA</a> - Protein Sequence Analysis for Sequences of Unknown Structure at <a href="http://bmerc-www.bu.edu/welcome.html">BMERC/MBCRR</a>

<a href="http://psort.nibb.ac.jp/">PSORT</a> - Predict Protein Sorting Signals Coded in Amino Acid Sequences at <a href="http://www.genome.ad.jp/">GenomeNet</a>, Japan

<a href="http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html">PSSP</a> - Protein Secondary Structure Prediction at <a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="></a>

<a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="> </a><a href="http://www.mcs.anl.gov/home/compbio/PUMA/Production/puma.html">PUMA</a> - Phylogeny of Unicellular Organims with Metabolism and Alignments from <a href="http://www.mcs.anl.gov/home/compbio/default.html">MCS-Computational Biology</a> at <a href="http://www.anl.gov/">Argonne National Laboratory</a>

<a href="file://ftp.embl-heidelberg.de/pub/databases/protein_extras/puu/domains.puu">PUU</a> - Protein Domains Database Based on PDB-Select at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://geta.life.uiuc.edu/index.html">RDP</a> - Ribosomal Database Project at U. Illinois

<a href="http://vent.neb.com/rebase/rebase.html">ReBase</a> - Restriction Enzyme Database and <a href="http://www.neb.com/cgi-bin/wais_ref.pl">ReBase-Search</a> at <a href="http://vent.neb.com/">New England Biolabs</a>, <a href="http://www.embl-heidelberg.de/srs/srsc?-id||777855676_129.186.4.14||-info||REBASE">ReBase</a> at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a> and <a href="http://www.gdb.org/Dan/rebase/rebase.html">ReBase</a> at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a>

<a href="http://www.embl-heidelberg.de/repro/rep_tot.html">REPRO</a> - Recognition of Protein Sequence Repeats at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://pundit.colorado.edu:8080/">RNA Secondary Structures</a> - Information on Group I Introns and rRNA at <a href="http://www.colorado.edu/">U. Colorado-Boulder</a>

<a href="http://www-rrna.uia.ac.be/rrna/index.html">rRNA</a> - Databases of Ribosomal Subunit RNA Sequences at <a href="http://www.uia.ac.be/">U. Antwerp</a>, Belgium

RSVP - Rapid Sequence Visualization in Postscript for Analysis of DNA Sequences at <a href="http://cbil.humgen.upenn.edu/">CBIL-U. Pennsylvania</a>

<a href="http://ulrec3.unil.ch/software/SAPS_form.html">SAPS</a> - Statistical Analysis of Protein Sequences at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland

<a href="http://base.icgeb.trieste.it/sbase/">SBASE</a> - Library of Protein Domains and <a href="http://base.icgeb.trieste.it/sbase/blast.html">SBASE-Search</a>  at <a href="http://base.icgeb.trieste.it/">ICGEB-Trieste</a>, Italy

<a href="http://geoff.biop.ox.ac.uk/servers/scanps_server.html">SCANPS</a> - Scan Protein Sequences at <a href="http://geoff.biop.ox.ac.uk/">U. Oxford</a>, UK

<a href="http://www.bio.cam.ac.uk/scop/">SCOP</a> - Structural Classification of Proteins at <a href="http://www.bio.cam.ac.uk/">Cambridge</a>, UK and <a href="http://www.nick.med.usf.edu/scop/index.html">SCOP</a> at <a href="http://www.nick.med.usf.edu/">U. South Florida</a>

<a href="http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html">Sequence Annotation</a> - Annotations on NCBI Sequences at <a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="></a>

<a images="" alt="(W3)" href="http://www.bcm.tmc.edu/%3EBaylor%20College%20of%20Medicine%3C/a%3E%20%3Cimg%20src="> </a><a href="http://alces.med.umn.edu/rawtrans.html">Sequence Translation</a> - Translate Gene Sequences at <a href="http://www.umn.edu/">U. Minnesota</a>

<a href="ftp://dasher.wustl.edu/pub/sleuth/data">Sleuth</a> - Amino Acid Conformation and Solvent Accessibility of PDB Files at <a href="http://ibc.wustl.edu/">Washington U.</a>

<a href="http://www.ibcp.fr/predict.html">SOPM</a> - Self Optimized Prediction Method for Prediction of Protein Secondary Structure at <a href="http://www.ibcp.fr/">IBCP-CNRS</a>, France

<a href="http://www.embl-heidelberg.de/srs/srsc">SRSWWW</a> - Network Browser for Databanks in Molecular Biology (w/ <a href="http://www.embl-heidelberg.de/srs/net.html">diagram links</a>) at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www.ch.embnet.org/srs/index.html">SRSWWW-Directory</a> - Directory of SRSWWW Network Browsers for Biological Databanks and <a href="http://www.ch.embnet.org/srs/status.html">SRSWWW-Global Status</a> at <a href="http://www.ch.embnet.org/">EMBnet-Basel</a>

<a href="http://genome.eerie.fr/fasta/ssearch-query.html">SSEARCH</a> - Universal Sequence Comparison Using the Smith-Waterman Algorithm at <a href="http://genome.eerie.fr/home.html">EERIE-Nimes</a>, France

<a href="http://www.embl-heidelberg.de/sspred/sspred_info.html">SSPRED</a> - Predict the Secondary Structure of Proteins at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>, Germany

<a href="http://www.embl-heidelberg.de/stride/stride.html">STRIDE</a> - Find Secondary Structural Elements in PDB Proteins Structures at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://www-genome.wi.mit.edu/cgi-bin/www-STS_Pipeline/pipeline_front">STS Pipeline</a> - Analysis and STS Primer Picking of Short DNA Sequences with Duplicate Checking, Sequence Repeat Finding, Restriction Analysis, Vector Identification and BLAST Searching at <a href="http://www-genome.wi.mit.edu/">MIT</a>

<a href="http://www.ucmb.ulb.ac.be/~joan/survol/form.html">SURVOL</a> - Analysis of Protein Atomic Volumes at <a href="http://www.ucmb.ulb.ac.be/">UCMB</a>, Belgium

<a href="http://expasy.hcuge.ch/ch2d/ch2d-top.html">Swiss-2DPage</a> - Two-dimensional Polyacrylamide Gel Electrophoresis Database at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland

<a href="http://www.ebi.ac.uk/srs/srsc?-info+SWISSDOM">SWISSDOM</a> - SwissProt Entries in a ProDom Map at <a href="http://www.ebi.ac.uk/">EBI</a>, UK

<a href="http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html">Swiss-Model</a>  - Automated Protein Modelling at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland

<a href="http://www.ebi.ac.uk/srs/srsc?-info||SWISSNEW">SWISSNEW</a> - New SwissProt Sequences at <a href="http://www.ebi.ac.uk/">EBI</a>, UK

<a href="http://expasy.hcuge.ch/sprot/sprot-top.html">SwissProt</a> - Protein Sequence Database (+ Weekly Updates) at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland

<a href="http://expasy.hcuge.ch/swisshop/SwissShopReq.html">Swiss-Shop</a>  - Automated SwissProt and Prosite Information Queries at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland

<a href="http://www.gdb.org/Dan/tbase/tbase.html">TBASE</a> - Transgenic/Targeted Mutation Database at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a>

<a href="http://genome.eerie.fr/fasta/tfasta-query.html">TFASTA</a> - Match a Protein Sequence Against All Six Frames of GenBank Sequences at <a href="http://genome.eerie.fr/home.html">EERIE-Nimes</a>, France

<a href="gopher://gopher.nih.gov/77/gopherlib/indices/tfd/index">TFD</a> - Transcription Factor Database at <a href="http://www.nih.gov/">NIH</a>

<a href="http://www.embl-heidelberg.de/srs/srsc?-info+TFFACTOR">TFFACTOR</a> and <a href="http://www.embl-heidelberg.de/srs/srsc?-info+TFSITE">TFSITE</a> - Transcription Factor Data at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://alces.med.umn.edu/rawtm.html">Tm</a> - Oligonucleotide Melting Point Determination at <a href="http://www.umn.edu/">U. Minnesota</a>

<a href="http://www.embl-heidelberg.de/tmap/tmap_sin.html">TMAP</a> - Identification of Transmembrane Segments on a Protein Sequence at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="ftp://ulrec3.unil.ch/pub/tmbase">TMBASE</a> - Transmembrane Protein Database at <a href="http://www.unil.ch/">U. Lausanne</a>, Switzerland

<a href="http://ulrec3.unil.ch/software/TMPRED_form.html">TMpred</a> - Prediction of Transmembrane Regions and Orientation in Protein Sequencs at <a href="http://ulrec3.unil.ch/">ISREC</a>, Switzerland

<a href="http://expasy.hcuge.ch/www/dna.html">Translate</a> - Translate a Nucleotide Sequence to a Protein at <a href="http://expasy.hcuge.ch/">ExPASy</a>, Switzerland

<a href="http://cbrg.inf.ethz.ch/subsection3_1_6.html">TreeGen</a> - Tree Generation from Distance Data at <a href="http://cbrg.inf.ethz.ch/">ETH-Zürich</a>, Switzerland

<a href="http://www.embl-heidelberg.de/srs/srsc?-id||781260221_129.186.4.14||-info||TREMBL">TREMBL</a> - Database of Translated Peptide Sequences of All CDS Features from EMBL Sequences at <a href="http://www.embl-heidelberg.de/">EMBL-Heidelberg</a>

<a href="http://cammsg3.caos.kun.nl:8000/srs/srsc?-info+VECBASE">VecBase</a> - Cloning Vector Sequence Database.at <a href="http://cammsg3.caos.kun.nl:8000/">CAOS/CAMM</a>, The Netherlands

<a href="http://biology.queensu.ca/~miseners/vector.html">Vector-DB</a> - Cloning Vector Database at <a href="http://www.queensu.ca/">Queen's U.-Kensington</a>, Canada , <a href="http://ben.vub.ac.be/srs/srsc?-info+VECTOR">VECTOR</a> at <a href="http://ben.vub.ac.be/">BEN</a>, Belgium , <a href="gopher://gopher.gdb.org/77/.INDEX/vector">Vector</a> at <a href="http://www.gdb.org/hopkins.html">Johns Hopkins</a> and <a href="gopher://virus1.virus.kyoto-u.ac.jp/77/.index/vector.ig/index">Vector-ig</a> at <a href="http://virus1.virus.kyoto-u.ac.jp/">IVR</a>, Kyoto-U., Japan

<a href="http://www.bio.cam.ac.uk/seqlogo/logo.cgi">WebLogo</a> - Sequence Logo Generation at <a href="http://www.bio.cam.ac.uk/">Cambridge U.</a>, UK

<a href="http://kestrel.ludwig.ucl.ac.uk/zpred.html">ZPRED</a> - MultPredict Secondary Structure of Multiply Aligned Protein Sequences at <a href="http://kestrel.ludwig.ucl.ac.uk/">Ludwig Institute for Cancer Research</a>, UK

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