[Bioperl-l] what format is this and how I can use AlignIO

[Guoneng Zhong]

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Hi,

Sorry for the ignorance on this matter.  I am trying to use the output 
of this standalone program called sim4 to create some sort of Alignment 
object.  The output looks like the following.  I thought perhaps BioPerl 
can give me an object that tells me exactly which nucleotide matches 
with which across the two aligned strands (that's what AlignIO does, 
right?).


seq1 = sim4seq4HyyX8K.seq, 2460 bp
seq2 = sim4seqOD34cJI.seq ((no header)), 876 bp


(complement)

       0     .    :    .    :    .    :    .    :    .    :
    1567 TGACAAGAGCACTGGCAAGGAGAACAAAATCACTATCACTAATGATAAGG
         ||||||||||||||||| |||||-|| ||||||||||  |   |  | |
       1 TGACAAGAGCACTGGCATGGAGA CAnAATCACTATCmcTanyGayAmGs

      50     .    :    .    :    .    :    .    :    .    :
    1617 GTCGTCTCAGCAAGGAGGACATTGAGCGCATGGTGCAGGAAGCTGAGAAG
         | ||||||||||||||||||||||||||||||||||||||||||||||||
      50 GtCGTCTCAGCAAGGAGGACATTGAGCGCATGGTGCAGGAAGCTGAGAAG

     100     .    :    .    :    .    :    .    :    .    :
    1667 TACAAGGCTGAGGATGATGTGCAGCGTGACAAGGTTTCTGCCAAGAACGG
         ||||||||||||||||||||||||||||||||||||||||||||||||||
     100 TACAAGGCTGAGGATGATGTGCAGCGTGACAAGGTTTCTGCCAAGAACGG

Any help?

Thanks,
G

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Hi,


Sorry for the ignorance on this matter.  I am trying to use the output
of this standalone program called sim4 to create some sort of
Alignment object.  The output looks like the following.  I thought
perhaps BioPerl can give me an object that tells me exactly which
nucleotide matches with which across the two aligned strands (that's
what AlignIO does, right?).


<fixed><fontfamily><param>Courier New</param>

seq1 = sim4seq4HyyX8K.seq, 2460 bp

seq2 = sim4seqOD34cJI.seq ((no header)), 876 bp



(complement)


      0     .    :    .    :    .    :    .    :    .    :

   1567 TGACAAGAGCACTGGCAAGGAGAACAAAATCACTATCACTAATGATAAGG

        ||||||||||||||||| |||||-|| ||||||||||  |   |  | | 

      1 TGACAAGAGCACTGGCATGGAGA CAnAATCACTATCmcTanyGayAmGs


     50     .    :    .    :    .    :    .    :    .    :

   1617 GTCGTCTCAGCAAGGAGGACATTGAGCGCATGGTGCAGGAAGCTGAGAAG

        | ||||||||||||||||||||||||||||||||||||||||||||||||

     50 GtCGTCTCAGCAAGGAGGACATTGAGCGCATGGTGCAGGAAGCTGAGAAG


    100     .    :    .    :    .    :    .    :    .    :

   1667 TACAAGGCTGAGGATGATGTGCAGCGTGACAAGGTTTCTGCCAAGAACGG

        ||||||||||||||||||||||||||||||||||||||||||||||||||

    100 TACAAGGCTGAGGATGATGTGCAGCGTGACAAGGTTTCTGCCAAGAACGG


Any help?


Thanks,

G</fontfamily></fixed>
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