Exact tandem repeats analyzer (E-TRA): A new program for DNA sequence mining

Abstract

Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as 'organs', 'tissues', 'cell lines' and 'development stages' for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.

Searching microsatellites in DNA sequences: approaches used and tools developed

“…This principle has been implemented by a number of investigators, but the most widely known example is that of Exact Tandem Repeats Analyzer (E-TRA) (Karaca et al 2005), which considers each of the nucleotide to be potentially a part of microsatellite and scans for the motif type as well as the length up to which it extends. Compound microsatellites are identified by measuring the distance between the two microsatellites with distance equaling zero.…”

Microsatellites for genetic and taxonomic research on thyme (Thymus L.)

“…Individual sequences of contigs and singletons were analyzed using the Exact Tandem Repeats Analyzer (e-TRA 1.0) program (Karaca et al, 2005a) to identify microsatellites. Microsatellites were considered to contain repeat motifs that were between 2 and 6 nucleotides in length.…”

E-microsatellite markers for some naturally occurring Salvia species in the Mediterranean region

“…Sequences of ESTs were analyzed using the Tandem Repeats Analyzer 1.5 software (Bilgen et al, 2004). In order to classify and detect microsatellites in ESTs, minimum motif length criteria were defined as being 10 repeats (20 bp) for dinucleotide, 7 repeats (21 bp) for trinucleotide, and 4 repeats for tetra-(16 bp), penta-(20 bp), and hexanucleotide (24 bp) motif lengths (Karaca et al, 2005a). After identification of ESTs containing microsatellites, they were assembled into contiguous sequences (contigs) using the Sequencher software (Gene Codes, Ann Arbor, MI, USA).…”