SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Functions of the protein "zinc finger and BTB domain-containing protein" Testtube General 0 08-31-2012 09:20 AM
download non redaudant protein sequence papori General 2 07-12-2012 10:24 PM
dna sequence to protein converter wijerasa Bioinformatics 1 01-13-2011 11:40 PM
Extract protein sequence from gff3 k-gun12 Bioinformatics 0 12-14-2010 10:56 AM
A simple question on cDNA and protein sequence cheng Bioinformatics 1 10-06-2010 08:36 PM

Reply
 
Thread Tools
Old 06-04-2013, 07:52 AM   #1
ajing
Junior Member
 
Location: Michigan

Join Date: Jan 2011
Posts: 3
Default How to make best guest of protein class from protein sequence

Hi,

I am not quit sure what the best way is to predict the name of protein class (e.g. Oxidoreductases) from protein sequence. Just Blast to the whole PDB and read some attributes of the result? Or very efficient way in biopython or other bioinformatics platform?
ajing is offline   Reply With Quote
Old 06-04-2013, 08:43 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,092
Default

If you doing this for a small number of sequences then that would be acceptable. How many are you looking at analyzing?

You can download the NCBI CDD database and do the searches locally if you have a large number of sequences: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/
GenoMax is offline   Reply With Quote
Old 06-04-2013, 09:44 AM   #3
ajing
Junior Member
 
Location: Michigan

Join Date: Jan 2011
Posts: 3
Default

Quote:
Originally Posted by GenoMax View Post
If you doing this for a small number of sequences then that would be acceptable. How many are you looking at analyzing?

You can download the NCBI CDD database and do the searches locally if you have a large number of sequences: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/
Thanks GenoMax,

Yes, CD-Search can help. I have thousands of sequence to search, so I want the process to be highly automatic. Could I ask an extented question? How could you find all related term for that protein after you search CDD database.
ajing is offline   Reply With Quote
Old 06-04-2013, 10:55 PM   #4
rhinoceros
Senior Member
 
Location: sub-surface moon base

Join Date: Apr 2013
Posts: 372
Default

Quote:
Originally Posted by ajing View Post
Thanks GenoMax,

Yes, CD-Search can help. I have thousands of sequence to search, so I want the process to be highly automatic. Could I ask an extented question? How could you find all related term for that protein after you search CDD database.
Consider blasting against the m5nr database. They should update it very soon..
rhinoceros is offline   Reply With Quote
Reply

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 07:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO