https://netbiolab.org/wiki/index.php?action=history&feed=atom&title=Finding_Interpro_annotation_without_BioMart 2026-05-15T20:51:27Z Revision history for this page on the wiki MediaWiki 1.31.16 https://netbiolab.org/wiki/index.php?title=Finding_Interpro_annotation_without_BioMart&diff=2731&oldid=prev 2013-04-18T16:41:00Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:41, 18 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site]</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2. Find out Uniprot protein IDs of the species &#160;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2. Find out Uniprot protein IDs of the species <ins class="diffchange diffchange-inline">that you want</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In case of Pseudomonas aeruginosa, the protein IDs of Pseudomonas Genome Database were different of their Uniprot proteins. Therefore, I downloaded Uniprot protein IDs of Pseudomonas aeruginosa at [http://www.uniprot.org/uniprot/ Uniprot homepage]. If you click [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&amp;format=* this URL], you can see my search result of Pseudomonas aeruginosa. &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In case of Pseudomonas aeruginosa, the protein IDs of Pseudomonas Genome Database were different of their Uniprot proteins. Therefore, I downloaded Uniprot protein IDs of Pseudomonas aeruginosa at [http://www.uniprot.org/uniprot/ Uniprot homepage]. If you click [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&amp;format=* this URL], you can see my search result of Pseudomonas aeruginosa. &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>3. From 'protein2ipr.dat.gz' file, extract only data with uniprot protein IDs of the species that you want to get. If you can use simple script languages, it is an easy job.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>3. From 'protein2ipr.dat.gz' file, extract only data with uniprot protein IDs of the species that you want to get. If you can use simple script languages, it is an easy job.</div></td></tr> </table>

Winnie https://netbiolab.org/wiki/index.php?title=Finding_Interpro_annotation_without_BioMart&diff=2730&oldid=prev 2013-04-18T16:38:49Z

<p>Created page with &quot;[http://www.ebi.ac.uk/interpro/ Interpro] annotation could be retrieved by [http://www.biomart.org/ BioMart]. But sometimes, in some species like Pseudomonas aeruginosa, BioMa...&quot;</p> <p><b>New page</b></p><div>[http://www.ebi.ac.uk/interpro/ Interpro] annotation could be retrieved by [http://www.biomart.org/ BioMart]. But sometimes, in some species like Pseudomonas aeruginosa, BioMart didn't provide Interpro annotation data. If then, follow the below three steps. <br /> <br /> 1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site]<br /> <br /> 2. Find out Uniprot protein IDs of the species <br /> In case of Pseudomonas aeruginosa, the protein IDs of Pseudomonas Genome Database were different of their Uniprot proteins. Therefore, I downloaded Uniprot protein IDs of Pseudomonas aeruginosa at [http://www.uniprot.org/uniprot/ Uniprot homepage]. If you click [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&amp;format=* this URL], you can see my search result of Pseudomonas aeruginosa. <br /> <br /> 3. From 'protein2ipr.dat.gz' file, extract only data with uniprot protein IDs of the species that you want to get. If you can use simple script languages, it is an easy job.</div>

Winnie