[Bioperl-l] remove gapped colums

James Wasmuth james.wasmuth at ed.ac.uk
Tue May 11 14:28:46 EDT 2004

 Hi Luisa,


$aln_nogaps = $aln->remove_columns(['gaps'])


"There are some days when I think I'm going to die from
an overdose of satisfaction."
         --- Salvador Dali

Nematode Bioinformatics                  |
Blaxter Nematode Genomics Group  |
School of Biological Sciences            |
Ashworth Laboratories                       | tel: +44 131 650 7403
University of Edinburgh                     | web: www.nematodes.org
Edinburgh                                            |
EH9 3JT                                               |
UK                                                       |   

luisa pugliese wrote:

 >   I am new at bioperl and I am working on alignments. I am splitting 
a multiple alignment into several pairwise alignments and I would like 
to remove the columns in which there are gaps in all the sequences. Does 
anybody knows if a method exists doing this or a method finding the 
columns in which there are gaps in all the sequences similar gap_line 
that find the gaps present in any columns?
 >Thank you
 >Luisa Pugliese
 >Luisa Pugliese, Ph.D.
 >luisa.pugliese at safan-bioinformatics.it
 >Corso Tazzoli 215/13 -10137 Torino
 >tel +39 011 3026230
 >cell. +39 333 6130644
 >Bioperl-l mailing list
 >Bioperl-l at portal.open-bio.org

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