ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.
One of the problems associated with the large-scale analysis of unannotated, low quality EST sequences is the detection of coding regions and the correction of frameshift errors that they often contain. We introduce a new type of hidden Markov model that explicitly deals with the possibility of errors in the sequence to analyze, and incorporates a method for correcting these errors. This model was implemented in an efficient and robust program, ESTScan. We show that ESTScan can detect and extract coding regions from low-quality sequences with high selectivity and sensitivity, and is able to accurately correct frameshift errors. In the framework of genome sequencing projects, ESTScan could become a very useful tool for gene discovery, for quality control, and for the assembly of contigs representing the coding regions of genes.
Iseli
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Swiss Institute of Bioinformatics, Epalinges, Switzerland. Christian.Iseli@isb-sib.ch
Jongeneel
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Bucher
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D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics; D005091:Exons; D020224:Expressed Sequence Tags; D015723:Gene Library; D008390:Markov Chains; D008969:Molecular Sequence Data; D016364:Reading Frames; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012984:Software
D018076:DNA, Complementary