Need a smith-Waterman that returns from/to in query and target sequences

Question

[juan.crescente]

I 'm looking for a smith.waterman implementation that given two sequences (and all respective parameters like match, mismatch/gap penalty and so) returns me the list of alignments and the begining and end in both sequences.

Implementations that do not do what we need:

• Biopython pairwise2 does not return that
• This c library neither ttps://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
• python's swalign https://pypi.python.org/pypi/swalign

Preferably should be a C library we can port into python, but given the things we found I don't think we are going to be so lucky.

[GenoMax]

Please do not delete posts that have already received answers.

Answer 1

[Pierre Lindenbaum]

not tested: there is an implementation of SW in BioJava: http://biojava.org/docs/api4.2.1/org/biojava/nbio/alignment/SmithWaterman.html

the method 'getPair' returns a http://biojava.org/docs/api4.2.1/org/biojava/nbio/core/alignment/template/SequencePair.html

with:

int     getIndexInQueryAt(int alignmentIndex)
Returns the query index corresponding to a given alignment column.
int     getIndexInQueryForTargetAt(int targetIndex)
Returns the query index corresponding to a given target index.
int     getIndexInTargetAt(int alignmentIndex)
Returns the target index corresponding to a given alignment column.
int     getIndexInTargetForQueryAt(int queryIndex)
Returns the target index corresponding to a given query index.

[juan.crescente]

I forgot to say no JAVA! thanks for the answer, is valid anyway

Answer 2

[Andrzej Zielezinski]

In my opinion, water from EMBOSS package (written in C) is one of the greatest implementions of the Smith-Waterman algorithm. If you are using Debian/Ubuntu, water is available as repository (named emboss).

Before you install it, you can check water on-line.

EDIT: I'm not sure whether water can report multiple alternative alignments (with the same scores).

[juan.crescente]

in I cannot find them in the results

Answer 3

[kyukokkyou999]

I've made a library implemented Smith-Waterman in python, and it must be helpful for you. => https://github.com/kyu999/ssw_aligner