[Bioperl-l] (no subject)

Diego Mauricio Riano Pachon diriano at uni-potsdam.de
Mon Jul 21 11:49:10 EDT 2008


Hi Ronnie,

Ronnie de Jonge wrote:
> Hi Dave, 
> Exactly my problem there in step 7 and 8. 
> As said, I tried to solve this problem by blasting the domain sequence to
> the cdna database, and use the first hit reference (parse by searchIO) for
> further truncation of the cdna hit. Though this gives false positives. 
>  
> -----
> I'm wonder now  if i could do the same, though instead of blasting the
> entire database just blast the hit to it's own cdna sequence (single fasta)
> 'on-the-fly'? (guess not possible, regarding the formatdb step?)
> -----

Yes, you can do this. using bl2seq (BLAST 2 sequences), something like:

Assuming that:

- $DNA has your Xn DNA sequence as a bioperl object, as in Dave e-mail.
- $protein_subseq has the SH2 domain from residue 30 to 51 from protein 
Xp, as a bioperl object

my $blast_factory= Bio::Tools::Run::StandAloneBlast->new(-program => 
'blastx', -F => 'F', -outfile => "$blast_output");
$blast_factory->bl2seq($DNA,$protein_subseq);

then you can parse the blast result using Bio::SearchIO.

hope this helps,

Diego

>  
> Cheers
> Ronnie
> 
>   _____  
> 
> From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave
> Messina
> Sent: maandag 21 juli 2008 17:04
> To: Dhr. R. de Jonge
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] (no subject)
> 
> 
> Okay, let me see if I've got this straight: you want to do Ka/Ks on just the
> subsequences of the cDNAs that match the HMMer domain?
> 
> 
> e.g.
> 1) You have a cDNA sequence. Let's call it Xn.
> 2) Xn is 300 nucleotides in length.
> 3) You translate Xn into protein Xp.
> 4) You use HMMer to search Xp against Pfam.
> 5) HMMer tells you that Xp has, for example, an SH2 domain from residue 30
> to residue 51.
> 6) Likewise, let's say two additional proteins Yp and Zp have the same SH2
> domain.
> 
> You want to:
> 7) Determine which nucleotides in Xn correspond to amino acids 30-51 in Xp.
> 8) Extract just those nucleotides (and also the nucleotides in Yn and Zn
> corresponding to their SH2 domain hits).
> 9) Align those nucleotide sequences.
> 10) Give the resulting multiple alignment to PAML and calculate the Ka/Ks
> ratios.
> 
> Is that correct?
> Is it steps 7 and 8 that you are trying to solve?
> 
> 
> 
> Dave
> 
> 
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> 


-- 
___________________________________
Diego Mauricio Riaño Pachón
Biologist - PhD student
AG Mueller-Roeber
Institute for Biochemistry and Biology
University of Potsdam

Address: Karl-Liebknecht-Str. 24-25
	 Haus 20
	 14476 Golm
	 Germany

Tel:	 +49 331 977 2809
Fax:	 +49 331 977 2512

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