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

Chris Fields cjfields at uiuc.edu
Tue Apr 22 14:58:40 EDT 2008


Related to that, I have thought about building a parser for some of  
the query-anchored alignments produced by blastall, just haven't had  
time to devote to it.  One of these days...

chris

On Apr 22, 2008, at 1:51 PM, Jason Stajich wrote:

> 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__
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
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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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