embl = new Array( "All", "Eukaryotes", "-Vertebrates", "--Mammals", "---Human", "---Rodents", "---Other mammals", "--Other vertebrates", "-Invertebrates", "-Fungi", "-Organelles", "-Plants", "Prokaryotes", "Bacteriophages", "Viruses", "Unclassified", "Synthetic", "GSS", "STS", "Patents" ); embl1 = new Array ( "embl-sp", "hum rod mam vrt inv fun org pln", "hum rod mam vrt", "hum rod mam", "hum", "rod", "mam", "vrt", "inv", "fun", "org", "pln", "pro", "phg", "vrl", "unc", "syn", "gss", "dbsts", "patent" ); htg = new Array( "All", "Eukaryotes", "-Vertebrates", "--Mammals", "---Human", "---Rodents", "----Mouse", "----Rat", "---Bovine", "---Other mammals", "--Zebrafish", "--Other vertebrates", "-Invertebrates", "--Drosophila", "--Other invertebrates", "-Plants", "--Arabidopsis", "--Other plants", "-Fungi", "Prokaryotes", "Unclassified" ); htg1 = new Array( "htg", "htg_hum htg_mus htg_rat htg_cow htg_mam htg_dan htg_vrt htg_dro htg_inv htg_ara htg_pln htg_fun", "htg_hum htg_mus htg_rat htg_cow htg_mam htg_dan htg_vrt", "htg_hum htg_mus htg_rat htg_cow htg_mam", "htg_hum", "htg_mus htg_rat", "htg_mus", "htg_rat", "htg_cow", "htg_mam", "htg_dan", "htg_vrt", "htg_dro htg_inv", "htg_dro", "htg_inv", "htg_ara htg_pln", "htg_ara", "htg_pln", "htg_fun", "htg_pro", "htg_unc" ); est = new Array( "All (non-redundant)", "Eukaryotes", "-Vertebrates", "--Mammals", "---Human", "---Rodents", "----Mouse", "----Rat", "----Other rodents", "---Bovine", "---Other mammals", "--Zebrafish", "--Other vertebrates", "-Invertebrates", "--Drosophila", "--Other invertebrates", "-Fungi", "-Plants", "--Arabidopsis", "--Other plants", "Prokaryotes" ); est1 = new Array( "est_nr", "est_hum est_mus est_rat est_rod est_cow est_mam est_dan est_vrt est_dro est_inv est_fun est_ara est_pln", // Eukaryotes "est_hum est_mus est_rat est_rod est_cow est_mam est_dan est_vrt", // -Vertebrates "est_hum est_mus est_rat est_rod est_cow est_mam", // --Mammals "est_hum", // ---Human "est_mus est_rat est_rod", // ---Rodents "est_mus", // ----Mouse "est_rat", // ----Rat "est_rod", // ----Other rodents "est_cow", // ---Bovine "est_mam", // ---Other mammals "est_dan", // --Zebrafish "est_vrt", // --Other vertebrates "est_dro est_inv", // -Invertebrates "est_dro", // --Drosophila "est_inv", // --Other invertebrates "est_fun", // -Fungi "est_ara est_pln", // -Plants "est_ara", // --Arabidopsis "est_pln", // --Other plants "est_pro" // Prokaryotes ); estug = new Array("All", "Human", "Mouse", "Rat", "Bovine", "Zebrafish"); estug1 = new Array("Hs_UG Mm_UG Rn_UG Bt_UG Dr_UG", "Hs_UG", "Mm_UG", "Rn_UG", "Bt_UG", "Dr_UG"); compgen = new Array("All", "Saccharomyces cerevisiae", "Schizosaccharomyces pombe", "Caenorhabditis elegans", "Arabidopsis thaliana", "All microbial genomes"); compgen1 = new Array("yeast pombe worm athseq bacteria", "yeast", "pombe", "worm", "athseq", "bacteria"); estcontigs = new Array("All", "Human", "Mouse", "Rat", "Bovine", "Zebrafish", "Drosophila", "Arabidopsis"); estcontigs1 = new Array("contigs", "Hs_contigs", "Mm_contigs", "Rn_contigs", "Bt_contigs", "Dr_contigs", "At_contigs", "Dm_contigs"); function setMenu(names, values) { document.form.nucldb.options.length = names.length; for (var i=0; i < names.length; i++) { document.form.nucldb.options[i].text = names[i]; document.form.nucldb.options[i].value = values[i]; } } function nucltypeChanged() { obj = document.form.nucltype; var txt = obj.options[obj.selectedIndex].text; objdb = document.form.nucldb; var prevdb = objdb.options[objdb.selectedIndex].text.toLowerCase(); var newdb; var newdb1; if (txt == "All EMBL + GSS (without HTG and ESTs)") { newdb=embl; newdb1=embl1; } else if (txt == "non-redundant dbEST") { newdb=est; newdb1=est1; } else if (txt == "dbEST") { newdb=est; newdb1=est1; } else if (txt == "Unigene EST") { newdb=estug; newdb1=estug1; } else if (txt == "Complete genomes") { newdb=compgen; newdb1=compgen1; } else if (txt == "Contigs EST") { newdb=estcontigs; newdb1=estcontigs1; } else if (txt == "HTG") { newdb=htg; newdb1=htg1; } else { obj2 = document.form.nucltype; document.form.nucldb.options.length = 1; document.form.nucldb.options[0].text = "N/A"; document.form.nucldb.options[0].value = obj2.options[obj2.selectedIndex].value; } document.form.nucldb.selectedIndex = 0; var exactmatch; //exact correspondence var approxmatch;//substring correspondence var categmatch; //taxonomic correspondence if (newdb) { //try to keep the previous nucldb selection while(prevdb.charAt(0) == "-") { prevdb = prevdb.substring(1,prevdb.length); } for(i=0; i

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Proteomics tools

Swiss-Prot

Mirror sites:

SIB BLAST Network Service

This NCBI BLAST2 service is maintained by the Swiss Institute of Bioinformatics on hardware kindly provided by .

Click on the icons to access the online BLAST help.

Accession number or sequence

Enter a Swiss-Prot/TrEMBL accession number or a PROTEIN sequence in RAW format.

Output format:

Choose the appropriate BLAST program and database:

blastp - query against a protein database

Taxonomic groups (not available for PDB and translated EST):

select a database subsection

To restrict the search to a particular taxon, it is much faster to select a database subsection from the drop-down list on the left than to specify your own taxonomic group in the box below. This also gives more accurate statistics.

or specify a taxonomic group

Enter a species name, a TaxID or the latin name of a taxonomic group (elements of the OC, OS and OX lines) to restrict your search to a particular taxon. You may enter a list separated by semicolons (";"). Example: Fungi; Homo sapiens.

or select a microbial proteome

Non-redundant Swiss-Prot+TrEMBL complete proteome sets, see the HAMAP pages.

Exclude fragment sequences (not available for PDB and translated EST)

tblastn - query against the six-frame translation of a nucleotide database document.write ("

\n"); document.write("Taxonomic groups:

or select a microbial genome

EMBL genome records, including plasmids.

Your email address: If an e-mail address is provided, results will be automatically mailed back (recommended for tblastn searches).

Options:

Comparison Matrix:
Number of best scoring sequences to show:
Number of best alignments to show:

Setting the E threshold: (Number of expected matches in a random database)

Filter the sequence for low-complexity regions

Gapped alignment

For a more 'advanced' BLAST2 search (with more options and programs, and a larger variety of databases) please use the original submission form at EMBnet-CH (Lausanne).