Difference between revisions of "Finding Interpro annotation without BioMart"
(Created page with "[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...") |
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1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site] | 1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site] | ||
| − | 2. Find out Uniprot protein IDs of the species | + | 2. Find out Uniprot protein IDs of the species that you want |
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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&format=* this URL], you can see my search result of Pseudomonas aeruginosa. | 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&format=* this URL], you can see my search result of Pseudomonas aeruginosa. | ||
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. | 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. | ||
Latest revision as of 01:41, 19 April 2013
Interpro annotation could be retrieved by BioMart. But sometimes, in some species like Pseudomonas aeruginosa, BioMart didn't provide Interpro annotation data. If then, follow the below three steps.
1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from Interpro download site
2. Find out Uniprot protein IDs of the species that you want
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 Uniprot homepage. If you click this URL, you can see my search result of Pseudomonas aeruginosa.
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.
