Kalaimathy, Singarevelu ; Sowdhamini, Ramanathan ; Kanagarajadurai, Karuppiah (2011) Critical assessment of structure-based sequence alignment methods at distant relationships Briefings in Bioinformatics, 12 (2). pp. 163-175. ISSN 1467-5463
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Official URL: http://bib.oxfordjournals.org/content/12/2/163.ful...
Related URL: http://dx.doi.org/10.1093/bib/bbq025
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.
| Item Type: | Article |
|---|---|
| Source: | Copyright of this article belongs to Oxford University Press. |
| Keywords: | Evolutionary Divergence; Protein Structures; Protein Domain Superfamilies; Evolutionary Relationships; Distantly Related Protein Domains |
| ID Code: | 97593 |
| Deposited On: | 13 Mar 2013 05:40 |
| Last Modified: | 13 Mar 2013 05:40 |
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