[Bioperl-l] Query seq with gaps in blast

[Julio Fernandez Banet]

Hello.
I would like to know how to get the subject sequence from an alignment with
gaps included.
As I'm trying to get the symbols in both sequences (query and subject) where
the homolog symbol is  " " I need to get the subject sequebce with gap to
get "-" when there and insertion in the query sequence.
It seems I get the gaps in the query (not sure) as The program gets "-"
symbol everytime there's a deletion and it only gives me an error with the
insertion.
Thanks a lot

My sequences to check the insertions are:
>seq 1
tcgccggcntcccggccaccctggtccccaggccccgtaccnctccgccaacgcctcgtcatggcngccccacnng
ccagcccagctggagggcacntgggcctgcccngcctgtgccctgcggctgctttgcagccacggaaacagcncac
cgtgctgctgggctttgaggcccaaccctggactgcggctgcctgggcgctatgaggtccgggcagaagtgggcaa
tggcgtgtccaggcacaacctctcctgcagcttttgacgtggtctccccagtggctgggctgcgggtcatcttacc
ctgccccccgcgacggccgccttctacgtgcccaccaacggctcagcctttggtgctccaggtggacttctggtgc
caacgccacggccacggcttcgcttggcctgggggcagtgtcagcgcccgcttttgagaaatgtctgccctgccct
ggtggccacctttcgtgcccggcttgcccctggga
>seq2
Tcgccggctcccggccaccctggtccccgggccccgtacctctccgccaacgcctcgtcatggctgccccacttgc
cagcccagctggagggcacttgggcctgccctgcctgtgccctgcggctgcttgcagccacggaacagctcaccgt
gctgctgggcttgaggcccaaccctggactgcggctgcctgggcgctatgaggtccgggcagaggtgggcaatggc
gtgtccaggcacaacctctcctgcagctttgacgtggtctccccagtggctgggctgcgggtcatctaccctgccc
cccgcgacggccgcctctacgtgcccaccaacggctcagccttggtgctccaggtggactctggtgccaacgccac
ggccacggctcgctggcctgggggcagtgtcagcgcccgctttgagaatgtctgccctgccctggtggccaccttc
gtgcccggctgcccctggga

The alignment is:
Query: 148   tcgccggcntcccggccaccctggtccccaggccccgtaccnctccgccaacgcctcgtc
207
             |||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||||
Sbjct: 24446 tcgccggc-tcccggccaccctggtccccgggccccgtacctctccgccaacgcctcgtc
24504

                   
Query: 208   atggcngccccacnngccagcccagctggagggcacntgggcctgcccngcctgtgccct
267
             ||||| |||||||  ||||||||||||||||||||| ||||||||||| |||||||||||
Sbjct: 24505 atggctgccccacttgccagcccagctggagggcacttgggcctgccctgcctgtgccct
24564

                   
Query: 268   gcggctgctttgcagccacggaaacagcncaccgtgctgctgggctttgaggcccaaccc
327
             |||||||| |||||||||||| |||||| |||||||||||||||| ||||||||||||||
Sbjct: 24565 gcggctgc-ttgcagccacgg-aacagctcaccgtgctgctgggc-ttgaggcccaaccc
24621

                   
Query: 328   tggactgcggctgcctgggcgctatgaggtccgggcagaagtgggcaatggcgtgtccag
387
             ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct: 24622 tggactgcggctgcctgggcgctatgaggtccgggcagaggtgggcaatggcgtgtccag
24681

                   
Query: 388   gcacaacctctcctgcagcttttgacgtggtctccccagtggctgggctgcgggtcatct
447
             ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct: 24682 gcacaacctctcctgcagc-tttgacgtggtctccccagtggctgggctgcgggtcatc-
24739

                   
Query: 448   taccctgccccccgcgacggccgccttctacgtgcccaccaacggctcagcctttggtgc
507
             ||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||
Sbjct: 24740 taccctgccccccgcgacggccgcc-tctacgtgcccaccaacggctcagcc-ttggtgc
24797

                   
Query: 508   tccaggtggacttctggtgccaacgccacggccacggcttcgcttggcctgggggcagtg
567
             ||||||||||| |||||||||||||||||||||||||| |||| ||||||||||||||||
Sbjct: 24798 tccaggtggac-tctggtgccaacgccacggccacggc-tcgc-tggcctgggggcagtg
24854

                   
Query: 568   tcagcgcccgcttttgagaaatgtctgccctgccctggtggccacctttcgtgcccggct
627
             ||||||||||| |||||| ||||||||||||||||||||||||||| ||||||||||||
Sbjct: 24855 tcagcgcccgc-tttgag-aatgtctgccctgccctggtggccacc-ttcgtgcccggc-
24910

                   
Query: 628   tgcccctggga 638
             |||||||||||
Sbjct: 24911 tgcccctggga 24921

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