Introducing variable gap penalties into three-sequence alignment for protein sequences

Che Lun Hung*, Chun Yuan Lin, Yeh Ching Chung, Chuan Yi Tang

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

6 Scopus citations

Abstract

The common-use gap penalty strategies, constant penalty and affine gap penalty, have been adopted in the traditional three-sequence alignment algorithm which considers the insertion, deletion and substitution. However, these strategies are not suitable to protein sequence alignments. For the alignment accuracy of protein sequences, the gap penalty is a major determinant. Incorporating protein structure information to vary the gap penalties can lead to more biologically correct alignments. Here, we present an algorithm to find a global and optimal alignment among three protein sequences by using position-specific gap penalties which allow gap penalties to be varied. Thus, residue-dependent information and protein structure information can be applied to the three-sequence alignment. The experimental results show that our algorithm achieves the significant improvement in the accuracy of alignments than the three-sequence alignment algorithm with the affine gap penalty for protein sequences.

Original languageEnglish
Title of host publicationProceedings - 22nd International Conference on Advanced Information Networking and Applications Workshops/Symposia, AINA 2008
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages726-731
Number of pages6
ISBN (Print)0769530966, 9780769530963
DOIs
StatePublished - 2008
Event22nd International Conference on Advanced Information Networking and Applications Workshops/Symposia, AINA 2008 - Gino-wan, Okinawa, Japan
Duration: 25 Mar 200828 Mar 2008

Publication series

NameProceedings - International Conference on Advanced Information Networking and Applications, AINA
ISSN (Print)1550-445X

Conference

Conference22nd International Conference on Advanced Information Networking and Applications Workshops/Symposia, AINA 2008
Country/TerritoryJapan
CityGino-wan, Okinawa
Period25/03/0828/03/08

Keywords

  • Dynamic programming
  • Sequence alignment
  • Three-sequence alignment
  • Variable gap penalties

Fingerprint

Dive into the research topics of 'Introducing variable gap penalties into three-sequence alignment for protein sequences'. Together they form a unique fingerprint.

Cite this