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71.
Ayse Gul Ince Mehmet Karaca Mehmet Bilgen A. Naci Onus 《Plant Cell, Tissue and Organ Culture》2008,94(3):281-290
Uniformly repeated DNA sequences in genomes known as tandem repeats are one of the most interesting features of many organisms
analyzed so far. Among the tandem repeats, microsatellites have attracted many researchers since their associations in several
human diseases. The discovery of tandem repeats in the expressed sequence tags (ESTs) or in the cDNA libraries contributed
to new ideas and tools for evolutionary studies. With the advent of new biotechnological tools the number of ESTs deposited
in databases is rapidly increasing. Therefore, new informative bioinformatics tools are needed to assist the analysis and
interpretation of these tandem repeats in ESTs and in other type of DNAs. In the present study we report two new utility tools;
Organism Miner and Keyword Finder. Organism Miner utility collects, sorts, splice and provides statistical overview on DNA
data files. Keyword Finder analyses all the sequences in the input folder and extracts and collects keywords for each specific
organism or the all the organisms, which have the DNA sequence and generates statistical overview. We are currently generating
cotton and pepper cDNA libraries and often using the GenBank DNA sequences. Therefore, in this study we used cDNAs and ESTs
of cotton and pepper for the demonstrating the use of these two tools. With help of these two utilities we observed that most
of ESTs are useful for downstream applications such as mining microsatellites specific to an organ, tissue or development
stage. The analyses of ESTs indicated that not only tandem repeats existed in ESTs but also tandem repeats differentially
presented in different organ or tissue specific ESTs within and between the species. Utilities and the sample data sets are
self-extracting files and freely available from or can be obtained upon request from the corresponding author. 相似文献