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      tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

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      Nucleic Acids Research

      Oxford University Press (OUP)

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          Abstract

          We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

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          Most cited references 26

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

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              dbEST--database for "expressed sequence tags".

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                Author and article information

                Journal
                Nucleic Acids Research
                Oxford University Press (OUP)
                0305-1048
                1362-4962
                March 1997
                March 01 1997
                March 01 1997
                March 1997
                March 01 1997
                March 01 1997
                : 25
                : 5
                : 955-964
                Affiliations
                [1 ]Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
                Article
                10.1093/nar/25.5.955
                146525
                9023104
                © 1997

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