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

Table 6 Average column scores of homologous region set

	Ref. 1.1	Ref. 1.2	Ref. 2	Ref. 3	Ref. 5	Overall	Ranksum
PEIME_piecewise	0.588	0.849	0.595	0.636	0.575	0.665	640
PRIME_affine	0.589	0.847	0.582	0.648	0.593	0.666	640
Prrn	0.561	0.834	0.601	0.630	0.558	0.654	708
MAFFT	0.552	0.846	0.532	0.631	0.578	0.640	670
ProbCons	0.591	0.875	0.540	0.625	0.583	0.658	548
T-Coffee	0.476	0.840	0.491	0.625	0.540	0.607	822
MUSCLE	0.496	0.823	0.496	0.574	0.501	0.596	946
DIALIGN-T	0.338	0.761	0.370	0.452	0.429	0.485	1339
POA	0.390	0.712	0.424	0.459	0.371	0.493	1348
ClustalW	0.416	0.791	0.443	0.475	0.394	0.529	1193

Each column shows average column scores using all alignments of each reference of the homologous region set. Overall and Ranksum columns show the average column scores and the rank sum of the Friedman test using all alignment of the whole homologous region set, respectively. A smaller rank sum means better accuracy.

ISSN: 1471-2105