Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

doi:10.1186/1471-2105-7-524

BMC Bioinformatics

Volume 7

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Research article

Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

Shinsuke Yamada¹^,2 , Osamu Gotoh²^,3 and Hayato Yamana¹

¹Department of Computer Science, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan

²Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan

³Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan

author email corresponding author email

BMC Bioinformatics 2006, 7:524doi:10.1186/1471-2105-7-524


Published:	1 December 2006

Additional files

Additional File 1:

PRIME source code. This tar.gz archive includes the source files of PRIME. To compile PRIME, one can check 'INSTALL' and 'Makefile' in the archive. Although 'Makefile' basically assumes GNU make and g+ +, another compiler can be used with a few modification of 'Makefile'.

Format: GZ Size: 48KB Download file

Additional File 2:

p-values of the Friedman test of full length set. Each value is p-value of the Friedman test, indicating the significance of a difference in performance between programs of a row and a column. The upper right and lower left p-values are calculated using sum-of-pairs and column scores on all alignments of the whole full length set, respectively. PRIME_pcwdenotes PRIME_piecewise, and PRIME_afn, PRIME_affine. The respective signs + and - denote that a program of a row performs significantly better and worse than that of a column.

Format: PDF Size: 32KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 3:

p-values of the Friedman test of homologous region set. Each value is p-value of the Friedman test, indicating the significance of a difference in performance between programs of a row and a column. The upper right and lower left p-values are calculated using sum-of-pairs and column scores on all alignments of the whole homologous region set, respectively. PRIME_pcwdenotes PRIME_piecewise, and PRIME_afn, PRIME_affine. The respective signs + and - denote that a program of a row performs significantly better and worse than that of a column.

Format: PDF Size: 32KB Download file

This file can be viewed with: Adobe Acrobat Reader