Fetching Domain Summary Information From Pfam In Bulk

Question

[Ananth]

Hi,

I'm interested in fetching the domain summary information from Pfam for a large number of protein families (around 3000). I am particularly looking for the organism related information present in the summary. For eg: DUF1013 is present in proteobacteria.

http://pfam.sanger.ac.uk/family?acc=PF06242

As I need this information for a large number of proteins, is there a way to download this info from Pfam ?

Answer 1

[Lars Juhl Jensen]

Did you try looking at the documentation of their REST API? A simple query like this can retrieve the information you want for one domain in a simple XML format:

http://pfam.sanger.ac.uk/family/PF06242?output=xml

All you have to do is to construct a ilst of such URLs for all your domains of interest and use curl or wget to fetch them.

[Ananth]

Thank you very much.

Answer 2

[Pierre Lindenbaum]

To complete Lars' answer, You can use the following XSLT stylesheet to directly extract the information you need:

<xsl:stylesheet xmlns:xsl="&lt;a href="http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform'
   xmlns:p="http://pfam.sanger.ac.uk/"
   version='1.0'
   >
<xsl:output method="text" encoding="UTF-8" indent="yes"/>

<xsl:template match="/">
<xsl:for-each select="p:pfam/p:entry">
<xsl:value-of select="@accession"/>
<xsl:text>  </xsl:text>
<xsl:value-of select="normalize-space(p:comment)"/>
<xsl:text>
</xsl:text>
</xsl:for-each>
</xsl:template>

</xsl:stylesheet>

eg:

for F in PF06141 PF03141 PF06242; do xsltproc stylesheet.xsl "http://pfam.sanger.ac.uk/family/${F}?output=xml"; done
PF06141  Tail fibre component U of bacteriophage.
PF03141  Members of this family of hypothetical plant proteins are probably methyltransferases: several of the aligned sequences either match the methyltransferase profile Profile:PS50124, or contain a SAM-binding motif Profile:PS50193. Swiss:Q9ZQ84 contains both. Several family members are described as ankyrin like.
PF06242  Family of uncharacterised proteins found in Proteobacteria.