[Bioperl-l] questions on Bio::Tools::Run::Alignment::Clustalw

[Dave Messina]

Hi Lorenzo,

Your code and data works for me with both clustalw v1.83 and 2.1. However, I
did have to change the name of the clustalw 2.1 executable from clustalw2 to
clustalw.

$ perl lorenzo.pl test_vs_test.besth.pep1.fas

 CLUSTAL 2.1 Multiple Sequence Alignments

Sequence format is Pearson
Sequence 1: gnl|Alyrata|AL6G05070   602 aa
Sequence 2: gnl|Alyrata|AL3G15690   611 aa
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score:  33
Guide tree file created:   [test_vs_test.besth.pep1.dnd]

There are 1 groups
Start of Multiple Alignment

Aligning...
Group 1: Sequences:   2      Score:6856
Alignment Score 1214

GCG-Alignment file created
 [/var/folders/Na/NagaNXNhHHm1GDx6seD-ME+++TI/-Tmp-/sniIE2msWJ/fGoixJVoUf]


--------------------- WARNING ---------------------
MSG: Use of method no_residues() is deprecated, use num_residues() instead
To be removed in 1.0075
---------------------------------------------------
34.8639455782313 and 625 and 1213





 What would be more efficient in term of memory usage:
> i.-performing the alignment directly over a fasta sequences file or
> ii.-performing the alignment over a ref to an array of seq objects:


Option i. But unless you're doing a ton, you probably won't notice either
way, so I would do whichever is more convenient.


Should I move the seqs files to the clustalw dir?
>

No, this isn't the problem. In the error message:
MSG: ClustalW call ( align
-infile="/Users/Lorenzo/Desktop/test_vs_test.besth.pep1.fas"
  -output=gcg
-outfile="/var/folders/rA/rApd7cXoFyWK-Yhn66cxZk+++TI/-Tmp-/O3Was62L0X/exicCvJnrF"
  2>&1) crashed: 32512

I notice that the path to your input file in that error is different than
the path in your code — perhaps this is the issue?


FInally, is there any way of geting the number of aminoacids in the aligned
> region in eg. the longer or the shorter sequence implemented or should I
> loop over the sequences in the $aln Bio::SimpleAlign object etc?.
>

I'm not sure I understand your question: do you want something different
than $aln->length() ?



Dave