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TreeFam treefam_scan.pl gene families

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diana_leduc

17 Nov, 2013 04:18 PM

I have run a the treefamsca.pl on the proteins from mouse. I get a couple of hits for each protein and transcript, but the problem is that once I run this protein on the online version I get a different result for the best matching family and the evalue score (ENSMUSG00000000001|ENSMUST00000000001 177 254 170 314 TF105461 27 104 29.7 6.5e-07, while on the online version TF300673 - evalue: 7e-207; bit-score: 690.3 400).
Is tehre any database with the Treefam identifiers and the name of the gene family.

Thank you in advance,

Diana

1. 1 Posted by mateus on 18 Nov, 2013 02:17 PM

   

   Hi Diana.

   Thanks for reporting that. We just updated the download session with the most up-to-date HMM library. Now you should obtain the same results for both treefamscan.pl and the webpage.

   Is tehre any database with the Treefam identifiers and the name of the gene family.

   Do you mean a list of all the gene names for each Treefam family? If so, the following file contains the information for both family IDs and gene names. You could parse these files, please let me know if you need help with that.

   http://www.treefam.org/static/download/treefam9_family_annotation.t...

   Do not hesitate in contacting us if you need any help.

   Cheers,

   Mateus.

   • Edit

2. 2 Posted by Diana LeDuc on 18 Nov, 2013 03:07 PM

   

   On November 18, 2013 at 3:17 PM mateus
   <[email blocked]> wrote:

   >
   > Hi Mateus,
   >

   Thank you for taking care of this so fast.

   I am actually looking for the description of the TF identifiers. The table that
   I find on http://www.treefam.org/browse under the Families section is just fine,
   but it seems that the description in the table provided for downloads is scarcer
   than on the web form.

   Thank you,

   Diana

   • Edit

3. 3 Posted by mateus on 18 Nov, 2013 04:51 PM

   

   Hi Diana.

   The table available in the download section, contains the following information:
   TF_name, fam_symbol, fam_description, numSequences, aln_len, aln_percent_identity, hgnc, pfam and numSpecies.

   Whereas in the "Browse" section only contains:
   ID, tax Distribution, #of genes, Identity, Aln length, HGNC Synbol and Description.

   The only information that you cant find in the downloadable version is the taxonomic level. Is that relevant for you right now?

   Also, be aware that for the browsable table, we we only display information for the families that where manually annotated (TF1*).

   Please let us know if you have any other queries.

   Mateus.

   • Edit

4. 4 Posted by Diana LeDuc on 26 Nov, 2013 08:12 PM

   

   On November 18, 2013 at 5:51 PM mateus
   <[email blocked]> wrote:

   >
   > Hi Mateus,
   >

   I now have another question regarding the Pfam hits for the TF identifiers. As I
   browse the web, I can find for each TF what Pfam family it hits (with %), but I
   haven't found the link to download this information. I am asking about this, as
   most of the TF families that are significant do not have a description.

   Thank you for your help.

   Diana

   • Edit

5. 5 Posted by mateus on 27 Nov, 2013 10:04 AM

   

   Hi Diana.

   You should be able to download that information from the download section (families with annotations):
   http://www.treefam.org/static/download/treefam9_family_annotation.t...

   Please let us know of any other queries.
   Mateus.

   • Edit

6. Matthieu Muffato closed this discussion on 08 Jun, 2015 02:02 PM.