pfam and treefam results differ

Jen Wyffels's Avatar

Jen Wyffels

23 May, 2013 09:02 PM

I used a FASTA protein file to search treefam and the result was PIK3R1/2/3 (TF102033) with SH2 included as a domain. When I use the same sequence and query pfam the results include SH2 & SOCS domains. This sequence has been identified through reciprocal blast to be SOCS6 which contains SH2 & SOCS domains. There exists a treefam TF321368 tree but it is not indicated by the sequence search. Please explain to me why the treefam search results do not recognize the SH2-SOCS domains and support homology. The attached file contains the sequence and screenshots from each site. Thank you

  1. Support Staff 1 Posted by mateus on 28 May, 2013 09:05 AM

    mateus's Avatar

    Hi Jen.
    There was a bug in the generation of some of the big families (>400 sequences) and they were not included in the HMM profile.
    Right now we are working on fixing it.
    We will get back to you as soon as this is fixed.
    Thank you for your contribution.
    Best regards,
    Mateus.

  2. Support Staff 2 Posted by mateus on 05 Jun, 2013 01:27 PM

    mateus's Avatar

    Hi Jen.
    We just fixed this problem.
    Some of our big alignments were failing to execute in our cluster due to memory limitations thus the HMM profiles were not being generated.
    Now, you should find the TreeFam family TF321368 as the first hit of your sequence.
    Best regards,
    Mateus.

  3. 3 Posted by Jennifer Wyffel... on 05 Jun, 2013 01:34 PM

    Jennifer Wyffels's Avatar

    Thats great! I plant to show the treefam results in a gene annotation page for a sequencing/community annotation project. I hope to write a script that will send a fasta sequence to the site and return the resulting tree for me to hyperlink. For now I am collecting the treefam sites manually but database planning begins next week. Best, Jen

  4. Support Staff 4 Posted by mateus on 05 Jun, 2013 02:01 PM

    mateus's Avatar

    Hi Jen.
    If you have any queries please do not hesitate in contacting us. We’ll be pleased to help.
    Best,
    Mateus.

  5. Matthieu Muffato closed this discussion on 08 Jun, 2015 01:59 PM.

Comments are currently closed for this discussion. You can start a new one.

Keyboard shortcuts

Generic

? Show this help
ESC Blurs the current field

Comment Form

r Focus the comment reply box
^ + ↩ Submit the comment

You can use Command ⌘ instead of Control ^ on Mac