[Bioperl-l] (no subject)
Diego Mauricio Riano Pachon
diriano at uni-potsdam.de
Mon Jul 21 11:49:10 EDT 2008
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:
- $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");
then you can parse the blast result using Bio::SearchIO.
hope this helps,
> From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave
> 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?
> 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
> 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
> Is that correct?
> Is it steps 7 and 8 that you are trying to solve?
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> Bioperl-l at lists.open-bio.org
Diego Mauricio Riaño Pachón
Biologist - PhD student
Institute for Biochemistry and Biology
University of Potsdam
Address: Karl-Liebknecht-Str. 24-25
Tel: +49 331 977 2809
Fax: +49 331 977 2512
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