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Bioinformatics Advance Access published online on July 15, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth410
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 22, 2004
Revised June 30, 2004
Accepted July 6, 2004

Article

A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences

Mehmet Bilgen 1, Mehmet Karaca 1*, A. Naci Onus 1, Ayse Gül Ince 1

1 Akdeniz University, Faculty of Agriculture, Antalya, 07059 Turkey

* To whom correspondence should be addressed. E-mail: mkaraca{at}akdeniz.edu.tr.


  Abstract

Motivation: One of the most interesting features of genomes (both coding and non-coding regions) is the presence of relatively short tandemly repeated DNA sequences known as Tandem Repeats (TRs). We developed a new PC based stand-alone software analysis program, combining sequence motif searches with keywords such as organs, tissues, cell lines or development stages for finding exact, inexact and compound tandem repeats. Tandem Repeats Analyzer 1.5 (TRA) has several advanced repeat search parameters/options over other repeat finder programs as it does not only accept GenBank, FASTA and EST sequence files but also does analysis of multi files with multi sequences. Advanced user defined parameters/options let the researchers use different motif lengths search criteria for varying motif lengths simultaneously. The outputs show statistical results to be evaluated by the user. The discovery of Tandem repeats in Expressed Sequence Tags (ESTs) could be useful for both gene mapping and association studies and discovering TRs located in coding regions of important genes that are expressed under various conditions of environment, stress, organ, tissue and development stage.

Results: In this paper we demonstrated applications of TRA using 175,899 Expressed Sequence Tags (ESTs) sequences for 3 Arabidopsis spp. downloaded from GenBank. The EST-SSRs/ESTs ratios were found 43.1%, 15.3%, and 2.34% in A. lyrata, A. thaliana and A. halleri, respectively. Analysis revealed that organs, tissues and development stages possessed different amounts of repeats and repeat compositions. This indicated that the distribution of tandem repeats among the tissues or organs may not be random differing from the untranscribed repeats found in genomes.

Availability: The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA.


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