Critical assessment of structure-based sequence alignment methods at distant relationships
Authors: Kalaimathy, Singarevelu; Sowdhamini, Ramanathan; Kanagarajadurai, Karuppiah
Source: Briefings in Bioinformatics, Volume 12, Number 2, 21 March 2011 , pp. 163-175(13)
Publisher: Oxford University Press
Abstract:Accurate sequence alignments are crucial for modelling and to provide an evolutionary picture of related proteins. It is well-known that alignments are hard to obtain during distant relationships. Three thousand and fifty-two alignments of 218 pairs of protein domain structural entries, with <40 sequence identity, belonging to different structural classes, of diverse domain sizes and length-rigid/variable domains were performed using 12 programs. Structural parameters such as root mean square deviation, secondary-structural content and equivalences were considered for critical assessment. Methods that compare fragments and permit twists and translations align well during distant relationships and length variations.
Document Type: Research Article
Publication date: 2011-03-21