[Biopython] pairwise sequence alignment programs in biopython

[John Berrisford]

Hi 

 

I'm looking at performing pairwise alignments of polymer sequences in
biopython. 

These will be protein or nucleotide sequences. They may include non-standard
residues which will be denoted as X. 

The sequences will be of varying length from around 20 residues up to
several thousand residues - put simply the range of sequences in the PDB. 

 

I'm looking for the best tool to use to do this in biopython

 

So far I have performed tests with pairwise2 and Align.PairwiseAligner. 

>From my tests it seems that pairwise2 has a limit of ~2000 residues - i.e.
if I give it a sequence of 2500 residues to compare against itself it
crashes. PairwiseAligner seems to be able to handle much longer sequences
without issue. 

 

I need to be able to set gap penalties - which is possible in both of these
programs. 

 

So my question are:

Are these the only options in biopython? - I would prefer a python
implementation rather than something that requires external compilation i.e.
Emboss Needle

Are these the best options?

Are they both maintained / stable? 

Are they comparable in their results?

Is the limitation in sequence length in pairwise2 a known issue? A quick
google search suggests most people use pairwise2, which is strange given its
sequence length limitation. 

 

Thank you

 

John 

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

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