[Bioperl-l] Fw: problem parsing msf file

[Mark A. Jensen]

neglected the list
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Paola Bisignano" <paola.bisignano at gmail.com>
Sent: Wednesday, September 23, 2009 9:04 AM
Subject: Re: [Bioperl-l] problem parsing msf file


> Hi Paola--
> I think you need column_from_residue_number() off the SimpleAlign object,
> and location_from_column off the LocatableSeq object. For your example, 
> try
> 
> $alnio = Bio::AlignIO->new( -file=>"my.msf");
> $aln = $alnio->next_aln;
> 
> $s1 = $aln->get_seq_by_pos(1);
> $s2 = $aln->get_seq_by_pos(2);
> 
> $col = $aln->column_from_residue_number( $s1->id, 28);
> $s2coord = $s2->location_from_column( $col - 1);
> 
> Now, $s2coord should equal 4 (the coordinate of the R before the I
> that aligns with the V in sequence 1).
> MAJ
> 
> 
> ----- Original Message ----- 
> From: "Paola Bisignano" <paola.bisignano at gmail.com>
> To: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at lists.open-bio.org>
> Sent: Friday, September 04, 2009 8:28 AM
> Subject: [Bioperl-l] problem parsing msf file
> 
> 
>>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
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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>> 
>>