Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
annotate hmmsearch results into fasta file (Read 19357 times)
Jun 12th, 2010 at 3:52am

Alekos   Offline
YaBB Newbies

Posts: 8
*
 
hi, i use UGENE and i find that is a very good help!

now im searching for proteins domains using hmmsearch against the proteome, the fasta/gb file is a list of proteins with the sequence, but what i need is to locate them in the genome, because i am working with domains, i dont think i could have problems with introns/exons. also, the translation of the file is quite possible, but how can i annotate the results of my hmmsearch in the genome??
 
IP Logged
 
Reply #1 - Jun 15th, 2010 at 8:27pm

Ivan Efremov   Offline
YaBB Administrator
Novosibirsk

Gender: male
Posts: 46
*****
 
Hi Alekos,

Could you please provide detailed step-by-step description of your work?
What is the difference between hmm search in fasta/gb files and hmm search in some 'genome'?

Thank you!


 

UGENE team
IP Logged
 
Reply #2 - Jun 18th, 2010 at 10:16pm

Alekos   Offline
YaBB Newbies

Posts: 8
*
 
well, im working looking for kinases involved in resistance genes in cassava, the thing is: i generate an hmm, hmmsearch in the proteome, and then, i want to locate those proteins in the genome
so i need the complete sequences of the hmmsearch result (it gives me only the sequences of the domains)
i had to do hmmsearch from console, output a table, import in a spreadsheet, copy.paste the protein names, search for those protein sequences with a perl script from mothur, and im refining the tblastn parameters
but hmm, i dont know if im doing something wrong, but the output of a hmmsearch made with ugene is the entire proteome!!

thank you in advance
 
IP Logged
 
Reply #3 - Jul 8th, 2010 at 2:50pm

Ivan Efremov   Offline
YaBB Administrator
Novosibirsk

Gender: male
Posts: 46
*****
 
Hi Alekos,

Quote:
 dont know if im doing something wrong, but the output of a hmmsearch made with ugene is the entire proteome!!


Could you please send us example of data files you use so we can reproduce the issue with 'entire proteome'?

As of finding complete sequences of found domains, it looks like a perfect task for UGENE Workflow Designer.
You can draw a schema, where domain sequences from HMM Search block are extracted using Sequence Splitter module and after that send to NCBI BLAST.
 

UGENE team
IP Logged
 
Page Index Toggle Pages: 1