title: A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA.
authors.affiliation: Faculty of Agriculture, Akdeniz University, 07059 Antalya, Turkey.
authors.forename: Mehmet
authors.initials: M
authors.lastname: Bilgen
authors.forename: Mehmet
authors.initials: M
authors.lastname: Karaca
authors.forename: A Naci
authors.initials: AN
authors.lastname: Onus
authors.forename: Ayşe Gül
authors.initials: AG
authors.lastname: Ince
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D020224:Expressed Sequence Tags; D018514:Plant Structures / Q000235:genetics*; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins