SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PFAM annotation - need help with awk scripting kmkocot Bioinformatics 0 05-04-2014 09:16 PM
Different between pfam and uniprot(swissprot) bongbimit Bioinformatics 1 03-18-2014 06:03 AM
1000 Genome data download for help? Peggy Liang Bioinformatics 0 11-14-2013 11:13 PM
hmmer and pfam rhinoceros Bioinformatics 2 06-11-2013 04:44 AM
Download of example Data Helicos Dolphin22 Helicos / Direct Genomics 1 10-24-2012 03:56 PM

Reply
 
Thread Tools
Old 05-09-2014, 12:49 PM   #1
bio_informatics
Senior Member
 
Location: USA

Join Date: Nov 2013
Posts: 182
Default download data from pfam

Dear Forum members,
I want to download the sequences or accession id from PFAM 7tm_1 for C. elegans.

Please help me how do proceed with this?
bio_informatics is offline   Reply With Quote
Old 05-09-2014, 02:24 PM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

Try UniProt

http://www.uniprot.org/

or BioMart.
mastal is offline   Reply With Quote
Old 05-09-2014, 06:01 PM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,973
Default

"7tm_1" Page: http://pfam.xfam.org/family/7tm_1

Click on "species" on the left. Find the C. elegans in the sunburst. Attaching an image to point to the area where you will find C. elegans (2 o'clock).

Once you select C. elegans, you can generate a file with fasta sequences by using the link in the "sunburst controls" panel (191 sequences).
Attached Images
File Type: gif pfam.gif (123.1 KB, 6 views)
GenoMax is offline   Reply With Quote
Old 05-09-2014, 06:24 PM   #4
bio_informatics
Senior Member
 
Location: USA

Join Date: Nov 2013
Posts: 182
Default

@Genomax: Wow. That is helpful. Thank you.
I got the organism. It shows 191 sequences, correctly.
When I click on generate Fasta file, it loads and further there is no activity.
Am I doing something wrong?

Last edited by bio_informatics; 05-09-2014 at 06:50 PM.
bio_informatics is offline   Reply With Quote
Old 05-10-2014, 05:25 AM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,973
Default

Quote:
Originally Posted by bio_informatics View Post
When I click on generate Fasta file, it loads and further there is no activity.
Am I doing something wrong?
You may need to allow pop-ups from the PFAM site, if you are using a blocker. I was able to download the file without any problems once I did that.
GenoMax is offline   Reply With Quote
Old 05-10-2014, 10:59 AM   #6
bio_informatics
Senior Member
 
Location: USA

Join Date: Nov 2013
Posts: 182
Default

Quote:
Originally Posted by GenoMax View Post
You may need to allow pop-ups from the PFAM site, if you are using a blocker. I was able to download the file without any problems once I did that.
some issue with Mozilla. Got it done with Chrome.

Thank you once again.
bio_informatics is offline   Reply With Quote
Reply

Tags
pfam

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO