MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of r

Background: Sequence alignment is one of the most important techniques to analyze biological systems. It is also true that the alignment is not complete and we have to develop it to look for more accurate method. In particular, an alignment for homologous sequences with low sequence similarity is not in satisfactory level. Usual methods for aligning protein sequences in recent years use a measure empirically determined. As an example, a measure is usually defined by a combination of two quantities (1) and (2) below: (1) the sum of substitutions between two residue segments, (2) the sum of gap penalties in insertion/deletion region. Such a measure is determined on the assumption that there is no an intersite correlation on the sequences. In this paper, we improve the alignment by taking the correlation of consecutive residues. Results: We introduced a new method of alignment, called MTRAP by introducing a metric defined on compound systems of two sequences. In the benchmark tests by PR...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Toshihide Hara, Keiko Sato, Masanori Ohya
• Keywords: BMCBI 2010, Low Sequence Similarity, Sequence Alignment, Sequences