I have a problem with bioperl sequence alignment files..but It can be reduced to a problem of how to manipulate string. I have this type of file...I'll paste below a pice of it 

                     1                                                
+   50
Sequence/23-178       NDPRVAAYGE VDELNSWVGY TKSLINSHTQ VLSNELEEIQ QLLF
+DCGHDL 
2zhz:A/1-148          DDARIAAIGD VDELNSQIGV L--LAEPLPD DVRAALSAIQ HDLF
+DLGGEL 


                      51                                              
+   100
Sequence/23-178       ATPADDERHS FKFKQEQPTV WLEEKIDNYT QVVPAVKKHI LPGG
+TQLASA 
2zhz:A/1-148          CIPGHAAITD AHLARLDG-- WLA----HYN GQLPPLEEFI LPGG
+ARGAAL

[download]

if I want to identify in that sequence which letter is at position 15 for example of "Sequence" and at the same position of the 2zhz" how can I count, walk...trough the sequence? Could anyone help me...I know I must use bioperl mailing list, but I've tried...actually noone replied and there aren't bioperl site as good as this web site. sorry also for my english...I'm trying to learn at the same time..bioinformatic, english and perl as well :-)

In reply to manipulating string by paola82

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