DNAlign TT: Pairwise DNA alignment with sequence specific transition-transversion ratio

Ankit Agrawal*, Huang Xiaoqiu

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Abstract

Pairwise DNA and protein sequence alignment is an important task in bioinformatics which forms the basis of many other tasks like multiple sequence alignment, protein structure and function prediction, phylogenetic analysis. In general, more emphasis is given to protein sequence alignment, and the alignment methods designed for protein sequences can usually be used with little modification for DNA sequences as well. However, it is desirable to design methods specifically for DNA alignments, making use of specific DNA sequence models and if possible, also of the specific sequences being aligned. In this paper, we present an iterative method for DNA sequence alignment with sequence specific transition-transversion ratio. Preliminary experiments indicate that the proposed technique has significant potential. The approach better suits to the nature of the specific DNA sequence pair, and could be a significant step in the direction of using sequence specific substitution matrices for DNA sequences.

Original languageEnglish (US)
Title of host publication2008 IEEE International Conference on Electro/Information Technology, IEEE EIT 2008 Conference
Pages453-455
Number of pages3
DOIs
StatePublished - Sep 15 2008
Event2008 IEEE International Conference on Electro/Information Technology, IEEE EIT 2008 Conference - Ames, IA, United States
Duration: May 18 2008May 20 2008

Publication series

Name2008 IEEE International Conference on Electro/Information Technology, IEEE EIT 2008 Conference

Other

Other2008 IEEE International Conference on Electro/Information Technology, IEEE EIT 2008 Conference
CountryUnited States
CityAmes, IA
Period5/18/085/20/08

ASJC Scopus subject areas

  • Information Systems and Management
  • Electrical and Electronic Engineering
  • Communication

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    Agrawal, A., & Xiaoqiu, H. (2008). DNAlign TT: Pairwise DNA alignment with sequence specific transition-transversion ratio. In 2008 IEEE International Conference on Electro/Information Technology, IEEE EIT 2008 Conference (pp. 453-455). [4554345] (2008 IEEE International Conference on Electro/Information Technology, IEEE EIT 2008 Conference). https://doi.org/10.1109/EIT.2008.4554345