[Biojava-l] Row order from multiple sequence alignment

Andreas Prlic andreas at sdsc.edu
Tue Mar 1 06:43:22 UTC 2016

Hi Spencer,

You might have to compare the accession codes of the sequences...

// 1 is the first sequence in the alignment, not 0...
 AlignedSequence<ProteinSequence, AminoAcidCompound> as =

Alternatively, what is the order of sequences that comes out of


On Mon, Feb 29, 2016 at 9:15 AM, Spencer Bliven <spencer.bliven at gmail.com>

> I'm creating a multiple sequence alignment using
> Alignments.getMultipleSequenceAlignment, as described in the cookbook
> <http://biojava.org/wiki/BioJava:CookBook3:MSA>. The problem is that the
> returned profile has rows in a different order than the input array of
> sequenced. How can I map from an index in the inputs to the rows of the
> profile?
> Thanks,
> Spencer
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Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
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