[Bioperl-l] problem parsing msf file

[Paola Bisignano]

I have a problem with the parsing of msf file...I can't find the exact
object of Bio::SimpleAlign for my case...
I have to identify residues (from a list) in aligned sequences...but
when I parse the alignment from fasta file, I save as msf file, where
I have to identify my residue (from the list, numbering as the pdb
file) and the residue aligned in the aligned sequences...

this is a piece of the file...

NoName   MSF: 2  Type: P  Wed Aug 26 10:32:50 2009  Check: 00 ..

 Name: Sequence/23-178  Len:    156  Check:  8937  Weight:  1.00
 Name: 2zhz:A/1-148     Len:    156  Check:  9006  Weight:  1.00

//


                      1                                                   50
Sequence/23-178       NDPRVAAYGE VDELNSWVGY TKSLINSHTQ VLSNELEEIQ QLLFDCGHDL
2zhz:A/1-148          DDARIAAIGD VDELNSQIGV L--LAEPLPD DVRAALSAIQ HDLFDLGGEL


                      51                                                 100
Sequence/23-178       ATPADDERHS FKFKQEQPTV WLEEKIDNYT QVVPAVKKHI LPGGTQLASA
2zhz:A/1-148          CIPGHAAITD AHLARLDG-- WLA----HYN GQLPPLEEFI LPGGARGAAL


                      101                                                150
Sequence/23-178       LHVARTITRR AERQIVQLMR EEQINQDVLI FINRLSDYFF AAARYANYLE
2zhz:A/1-148          AHVCRTVCRR AERSIVALGA SEPLNAAPRR YVNRLSDLLF VLARVLNRAA


                      151                                                200
Sequence/23-178       QQPDML
2zhz:A/1-148          GGADVL

for example in this I have to identify the residue that is in front of
Val 28 (that is in Sequen) in 2zhz:A (that manually conting is Ile
5)....
Tyr4-> has no residue in front of it because the alignment starts from
N23 of Sequence...
how can I find the way to enter the residue of my sequen, and extract
the residue from the other????


I wish you all dear friends..and I'm actually in atrouble with this..
Thanks for suggestions

Paola