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

Jason Stajich jason at bioperl.org
Tue Apr 22 14:51:08 EDT 2008


if you get it as axt it should parse fine in SearchIO but that is  
pairwise, if you can get an alignment blocks I can't remember what  
format this is from UCSC.
MSAs are going to be better handed through Bio::AlignIO though so it  
might be better to build a parser on that.

On Apr 22, 2008, at 7:22 AM, Chris Fields wrote:

> 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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