[Bioperl-l] parsing msf file (sorry last question about it)

[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