SeqAlign.jl
Simple program to align sequences in Julia
Overview
This code provides two main functions, smithwaterman(seq1::String, seq2::String, and needlemanwunsch(seq1::String, seq2::String)
(respectively local sequence alignment, global sequence alignment).
Allowed seq1,seq2 are just for DNA,RNA sequences (ACGT,acgt,ACGU,
acgu, or mixed capitalization). Score matrix is built in. So far the
program compute equivalent optimal solutions only for local alignments
(smithwaterman) but not yet for global alignment (needlemanwunsh).
The output is Array{(String,String,String),1} where the first two
strings represent the alignment, and the third a vector of symbols:
+ = match, o = not match, - = insert
Usage
Just type using SeqAlign at julia prompt
Todos
Protein sequences, custom score matrices.