PRIME website

PRIME is a multiple sequence alignment program that employs doubly nested randomized iterative refinement strategy, and written in ISO standard C++. The crucial feature of PRIME is a group-to-group sequence alignment algorithm with piecewise linear gap cost, instead of traditional affine gap cost.

Current Release (Updated: 15, Jul 2007):

• prime-1.1.tar.gz (MD5: 0dc36a27a6d1667fc20e51cdb1c17d4d)

Previous Release:

• prime-1.0.tar.gz (MD5: 0eafc1d939072d442cb3acb337a0072f)

To begin with, extract gzipped tar archive: Set compile options if needed, and compile the source codes: Then, copy prime binary into your favorite directory. For detailed compile options, see `Makefile'.

The basic usage is: All options are shown in the man page for prime(1). Two simple examples are given below.

If you simply align the sequences in the file `input' without specifying any options, then: In this case, the result will be printed in the standard output.

If you align the sequences in `input' with `BLOSUM62' matrix and gap cost specified by `gparam' and make sure that the result will be written to the file `output':

1. Yamada,S., Gotoh,O. and Yamana,H. (2006) Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost, BMC Bioinformatics, 7, 524.
2. Gotoh,O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments, J. Mol. Biol., 264, 823-838.
3. Gotoh,O. (1990) Optimal sequence alignment allowing for long gaps, Bull. Math. Biol., 52, 359-373.
4. Gotoh,O. (1993) Optimal alignment between groups of sequences and its application to multiple sequence alignment, Comput. Appl. Biosci., 9, 361-370.
5. Gotoh,O. (1994) Further improvement in methods of group-to-group sequence alignment with generalized profile operations, Comput. Appl. Biosci., 10, 379-387.

PRIME-related websites:

• PRIME mirror site (Waseda University)
• ALN website

Institution and Laboratory websites:

• Computational Biology Research Center
• Gotoh Laboratory (Kyoto University)
• Yamana Laboratory (Waseda University)

If you have any problems or comments, please don't hesitate to send an e-mail.