Presence of proteins in a group of organisms
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6 weeks ago

I need to estimate the presence of some proteins in a group of bacteria (~100-200 species). I have their taxids and chromosome accessions. I don't want to do it manually through the web blast and I decided to use blast+ and restrict its search to this bacteria by their taxids, but I found out that this is impossible by remote blast search. I don't want to make a local database too:) Are there any other ways to do it? enter image description here

proteins restriction BLAST • 157 views
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6 weeks ago
Mensur Dlakic ★ 12k

If your protein of interest is in Pfam, the results may already be pre-calculated. Let's say that this is your protein family. On the left-hand side in that page there is a Species link where you can see a species distribution of that family, either in sunburst form or as a tree.

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In addition, there are several databases of orthologous genes, such as OMA and OrthoDB, which probably also have this information.

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