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

Edward Wijaya ewijaya at gmail.com
Tue Apr 22 10:03:07 EDT 2008


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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