[Bioperl-l] parsing msf file

[Paola Bisignano]

Hi dear friends,

I used Bio::AlignIO to parse msf file, using method
colum_from_residue_number, as you suggested to obtain the position in
the alignment of  residues of interest (in contact with my ligand) and
I have to do a check of the residue:
I want to extract the type of the residue...I ask my question using
the number of the residue in the PDB, and i want the script return
also the residue so if I want to know the position af ala21, I  will
do:

my $alnio = Bio::AlignIO->new( -file=>"my file.msf");
my $aln = $alnio->next_aln;

my $s1 = $aln->get_seq_by_pos(1);
my $s2 = $aln->get_seq_by_pos(2);

my $col = $aln->column_from_residue_number( $s1->id, 21)

and It will return the position (es. 5) but I want to check if in
position 5 of the alignment there is A (for ala)....I looked in
documentation, but I couldn't find anything for that


Thank you all for help you gave and will give to me,

best regards,

paola