[Bioperl-l] BioPerl Module to Parse BLAT alignment output

Chris Fields cjfields at uiuc.edu
Tue Apr 22 10:59:25 EDT 2008


A quick grep of bioperl-live gets me Bio::SearchIO::blast,  
Bio::SearchIO::axt, Bio::SearchIO::psl, Bio::Tools::Blat, and  
Bio::Tools::WebBlat.  Haven't looked at the docs but it's a start!

chris

On Apr 22, 2008, at 9:03 AM, Edward Wijaya wrote:

> Hi,
>
> Is there any module that can parse the following output
> of BLAT. This is taken from UCSC browser.
>
> The idea is to parse it and then extract the conserved block
> of aligned sequences.
>
>
> __DATA__
> Alignment block 3 of 135 in window, 5860248 - 5860300, 53 bps
> B D   D. melanogaster
> tgtg----tatttatgt-tttaaataaaggt-------tttctaaata---cgaaatttcaaatttaa
> B D       D. simulans
> tgtg----tatttatgt-tttaaataaaggt-------tttttaaata---cgcaattttaaatttaa
> B D      D. sechellia
> tgtg----tatttatgt-tttaaataaaggt-------tttttaaata---cccaattttaaatttaa
> B D         D. yakuba
> tgtg----tatttatgt-tcttaataaaggt-------ttcctaaataa-ttcaaaatttaaattaaa
>           D. erecta
> tgtg----tgtttatgt-ttttaataaaggt-------tttctaaataa--tcgaaattcatttcaaa
>        D. ananassae
> taag----tttttatgtattttaaaatatag-------aaaataaata---aaaaaaattgaact---
>    D. pseudoobscura
> tata----ccagtacac-cttatatg------------tttttaaata--------------------
> B D     D. persimilis
> tata----ccagtacac-attatatg------------tttttaaata--------------------
>       D. willistoni
> aaaaaagttatttgaat-ttggaata------------taccaaaacatgttggaaatt------gaa
>          D. virilis
> -------------gatt-ttataataaaattgcgctaatttctaa------------tttacgttaaa
>       D. mojavensis
> -------------tagt-ccttaatataaatataatattaaataaata-------cttttaagttaaa
>        D. grimshawi
> ====================================================================
>        T. castaneum
> ====================================================================
>
> Inserts between block 3 and 4 in window
>   D. pseudoobscura 2008bp
> B D    D. persimilis 1421bp
>         D. virilis 5bp
>      D. mojavensis 4640bp
>
> Alignment block 4 of 135 in window, 5860301 - 5860344, 44 bps
> B D   D. melanogaster
> ----tgggtagcagcgttgccagat--------------------aaagggacatgtttactggctga
> B D       D. simulans
> ----tgggaagcagcgttgccagat-------------------gaaacgggcatgtttgcaggctga
> B D      D. sechellia
> ----tgggaagcagcgttgccagat-------------------gaaacgggcatgtttgcaggctga
> B D         D. yakuba
> ----tgagtaccaatgctgccagat-------------ctttgtaaagcggtaatgtttgctggctga
>           D. erecta
> ----t-----ttaatgttgccagat-------------ctgcgtaaggcgctcatgttggctggctga
>    D. pseudoobscura
> ====================================================================
> B D     D. persimilis
> ====================================================================
>       D. willistoni
> ----aggattacgaagttcctttat-------------------aaag--------------------
>          D. virilis
> gactagtttaatatctcagcccgttaagctaactgttactttttacagtattcgcgccattttgc---
>       D. mojavensis
> ====================================================================
>        D. grimshawi
> ====================================================================
>        T. castaneum
> ====================================================================
>
> __ END__
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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