tag:treefam.tenderapp.com,2013-02-16:/discussions/questions/60-treefam-treefam_scanpl-gene-familiesTreeFam: Discussion 2015-06-08T14:02:58Ztag:treefam.tenderapp.com,2013-02-16:Comment/300373582013-11-17T16:18:39Z2013-11-17T16:18:40ZTreeFam treefam_scan.pl gene families<div><p>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).<br>
Is tehre any database with the Treefam identifiers and the name of
the gene family.</p>
<p>Thank you in advance,</p>
<p>Diana</p></div>tag:treefam.tenderapp.com,2013-02-16:Comment/300373582013-11-18T14:17:38Z2013-11-18T14:17:38ZTreeFam treefam_scan.pl gene families<div><p>Hi Diana.</p>
<p>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.</p>
<blockquote>
<p>Is tehre any database with the Treefam identifiers and the name
of the gene family.</p>
</blockquote>
<p>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.</p>
<p><a href=
"http://www.treefam.org/static/download/treefam9_family_annotation.tab.tar">
http://www.treefam.org/static/download/treefam9_family_annotation.t...</a></p>
<p>Do not hesitate in contacting us if you need any help.</p>
<p>Cheers,</p>
<p>Mateus.</p></div>mateustag:treefam.tenderapp.com,2013-02-16:Comment/300373582013-11-18T15:07:16Z2013-11-18T15:07:17ZTreeFam treefam_scan.pl gene families<div><p>On November 18, 2013 at 3:17 PM mateus<br>
<a href=
"mailto:tender2+dae2b26dfa25108c48c588e95d9a21e459f9a2230@tenderapp.com">
tender2+dae2b26dfa25108c48c588e95d9a21e459f9a2230@tenderapp.com</a>
wrote:</p>
<blockquote>
<p>Hi Mateus,</p>
</blockquote>
<p>Thank you for taking care of this so fast.</p>
<p>I am actually looking for the description of the TF identifiers.
The table that<br>
I find on <a href=
"http://www.treefam.org/browse">http://www.treefam.org/browse</a>
under the Families section is just fine,<br>
but it seems that the description in the table provided for
downloads is scarcer<br>
than on the web form.</p>
<p>Thank you,</p>
<p>Diana</p></div>Diana LeDuctag:treefam.tenderapp.com,2013-02-16:Comment/300373582013-11-18T16:51:17Z2013-11-18T16:51:17ZTreeFam treefam_scan.pl gene families<div><p>Hi Diana.</p>
<p>The table available in the download section, contains the
following information:<br>
TF_name, fam_symbol, fam_description, numSequences, aln_len,
aln_percent_identity, hgnc, pfam and numSpecies.</p>
<p>Whereas in the "Browse" section only contains:<br>
ID, tax Distribution, #of genes, Identity, Aln length, HGNC Synbol
and Description.</p>
<p>The only information that you cant find in the downloadable
version is the taxonomic level. Is that relevant for you right
now?</p>
<p>Also, be aware that for the browsable table, we we only display
information for the families that where manually annotated
(TF1*).</p>
<p>Please let us know if you have any other queries.</p>
<p>Mateus.</p></div>mateustag:treefam.tenderapp.com,2013-02-16:Comment/300373582013-11-26T20:12:36Z2013-11-26T20:12:37ZTreeFam treefam_scan.pl gene families<div><p>On November 18, 2013 at 5:51 PM mateus<br>
<a href=
"mailto:tender2+dae2b26dfa25108c48c588e95d9a21e459f9a2230@tenderapp.com">
tender2+dae2b26dfa25108c48c588e95d9a21e459f9a2230@tenderapp.com</a>
wrote:</p>
<blockquote>
<p>Hi Mateus,</p>
</blockquote>
<p>I now have another question regarding the Pfam hits for the TF
identifiers. As I<br>
browse the web, I can find for each TF what Pfam family it hits
(with %), but I<br>
haven't found the link to download this information. I am asking
about this, as<br>
most of the TF families that are significant do not have a
description.</p>
<p>Thank you for your help.</p>
<p>Diana</p></div>Diana LeDuctag:treefam.tenderapp.com,2013-02-16:Comment/300373582013-11-27T10:04:45Z2013-11-27T10:04:45ZTreeFam treefam_scan.pl gene families<div><p>Hi Diana.</p>
<p>You should be able to download that information from the
download section (families with annotations):<br>
<a href=
"http://www.treefam.org/static/download/treefam9_family_annotation.tab.tar">
http://www.treefam.org/static/download/treefam9_family_annotation.t...</a></p>
<p>Please let us know of any other queries.<br>
Mateus.</p></div>mateus