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/* * align2seq * * Functions to perform sequence alignment directly in PostgreSQL * Andre Masella <email@example.com> */ 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.