[Bioperl-l] problem parsing msf....:second part...I cannot solve sorry sorry

[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