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Sequence alignment module for PostgreSQL
C
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debian
Makefile
README.align2seq
align2seq.c
align2seq.sql.in
align2seq_uninstall.sql.in

README.align2seq

/*
 * align2seq
 *
 * Functions to perform sequence alignment directly in PostgreSQL
 * Andre Masella <andre@masella.no-ip.org>
 */

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.
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