Title

SeqMaT: A sequence manipulation tool for phylogenetic analysis 

Authors

Pavan Kumar Attaluri¹, Mary C Christman², Zhengxin Chen¹, Guoqing Lu²*

Affiliation

¹Department of Computer Science; ²Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA 

Email

glu3@unomaha.edu; *Corresponding author  

1-402-5543195

1-402-5543532

Article Type

Software

Date

Received December 23, 2010; Accepted January 01, 2011; Published February 07, 2011
 

Most bioinformatics tools require specialized input formats for sequence comparison and analysis. This is particularly true for molecular phylogeny programs, which accept only certain formats. In addition, it is often necessary to eliminate highly similar sequences among the input, especially when the dataset is large. Moreover, most programs have restrictions upon the sequence name. Here we introduce SeqMaT, a Sequence Manipulation Tool. It has the following functions: 1) data format conversion, 2) sequence name coding and decoding, 3) redundant and highly similar sequence removal, and 4) data mining utilities. SeqMaT was developed using Java with two versions, web-based and standalone. A standalone program is convenient to manipulate a large number of sequences, while the web version will guarantee wide availability of the tool for researchers and practitioners throughout the Internet.  

Availability

http://glee.ist.unomaha.edu/seqmat

Keywords

SeqMaT, format conversion, phylogeny, data mining

Citation

Attaluri et al. Bioinformation 5(9): 400-401 (2011)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.