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The problem of predicting gene locations in newly sequenced DNA is well known but still far from being successfully resolved. A novel approach to the problem based on the frame dependent (non-homogeneous) Markov chain models of protein-coding regions was previously suggested. This approach is, apparently, one of the most powerful "search by content"(More)
We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed to bypass this difficulty, one effective(More)
The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and(More)
BACKGROUND The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous) proteins is not available, while algorithms of the second type imply that information(More)
The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed and tuned for gene prediction in(More)
Finding new protein-coding genes is one of the most important goals of eukaryotic genome sequencing projects. However, genomic organization of novel eukaryotic genomes is diverse and ab initio gene finding tools tuned up for previously studied species are rarely suitable for efficacious gene hunting in DNA sequences of a new genome. Gene identification(More)
BACKGROUND The 1.83 Megabase (Mb) sequence of the Haemophilus influenzae chromosome, the first completed genome sequence of a cellular life form, has been recently reported. Approximately 75 % of the 4.7 Mb genome sequence of Escherichia coli is also available. The life styles of the two bacteria are very different - H. influenzae is an obligate parasite(More)
MOTIVATION Markov chain models of DNA sequences have frequently been used in gene finding algorithms. Performance of the algorithm critically depends on the model structure and parameters. Still, the issue of choosing the model structure has not been studied with sufficient attention. RESULTS We have assessed performance of several types of Markov chain(More)
BACKGROUND Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary mechanism by which retrotransposons contribute to structural gene evolution is through insertion into an intron or a gene flanking region, and subsequent incorporation into an exon. (More)
One of the major goals of computational sequence analysis is to find sequence similarities, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations among the sequences. Since the degree of similarity is usually assessed by the sequence alignment score, it is necessary to know if a score is high enough to(More)