Bioinformatics Advance Access originally published online on July 15, 2004
Bioinformatics 2004 20(18):3379-3386; doi:10.1093/bioinformatics/bth410
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences
e Gül Ince
Faculty of Agriculture, Akdeniz University, 07059 Antalya, Turkey
Received on April 22, 2004; revised on June 30, 2004; accepted on July 6, 2004
Advance Access Publication July 15, 2004
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, TRs. 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 expressed sequence tag (EST) sequence files but also does analysis of multifiles with multisequences. 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 TRs in 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 ESTs sequences for three 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 TRs 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
Contact: mkaraca{at}akdeniz.edu.tr
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.