/*

• align2seq
• Functions to perform sequence alignment directly in PostgreSQL
• Andre Masella [email protected] */

Release Notes: Version 0.1

• Initial release

Installation: In this directory run:

make
make install

You can use align2seq.sql to create the functions in your database of choice, e.g.

psql template1 < align2seq.sql

installs align2seq functions into database template1

Documentation:

FUNCTION align_n(text, text) RETURNS int4

Align two nucleotide sequences using the Smith-Waterman algorithm and return the alignment score. The score will always be non-negative.

FUNCTION align_p(text, text) RETURNS int4

Align two aminoacid sequences using the Smith-Waterman algorithm and return the alignment score. The score will always be non-negative.

FUNCTION n2p(text, int4) RETURNS text

Convert a nucleotide sequence to a protein sequence. The numeric parameter skips the first n nucleotides of the sequence, used for shifting the reading frame.