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Literature DB >> 8374073

Recognition of genes in DNA sequence with ambiguities.

Abstract

The search for genes in a newly sequenced DNA is a well known problem. Among other factors, the gene-searching process is hampered by a number of ambiguities which may remain unresolved experimentally for a long time. A computer method that is able to predict genes in a DNA sequence containing ambiguities has been developed, based on the non-homogeneous Markov chain technique. The reliability of the method has been tested using a set of sequences generated by a Monte-Carlo procedure and a set of 425 E. coli sequences with ambiguities introduced artificially.

Entities: Species

Mesh：

Substances：
DNA, Bacterial
DNA

Year: 1993 PMID： 8374073 DOI： 10.1016/0303-2647(93)90068-n

Source DB: PubMed Journal: Biosystems ISSN： 0303-2647 Impact factor: 1.973

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Cited

35 in total

1. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.

Authors: Ritu Pandey; Andreas Müller; Carolyn A Napoli; David A Selinger; Craig S Pikaard; Eric J Richards; Judith Bender; David W Mount; Richard A Jorgensen
Journal: Nucleic Acids Res Date: 2002-12-01 Impact factor: 16.971

2. Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate.

Authors: Rosanna A Alegado; Steven Ferriera; Chad Nusbaum; Sarah K Young; Qian Zeng; Alma Imamovic; Stephen R Fairclough; Nicole King
Journal: J Bacteriol Date: 2010-12-23 Impact factor: 3.490

3. Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.

Authors: Michaël Bekaert; Hugues Richard; Bernard Prum; Jean-Pierre Rousset
Journal: Genome Res Date: 2005-10 Impact factor: 9.043

4. Prevalence of ColE1-like plasmids and colicin K production among uropathogenic Escherichia coli strains and quantification of inhibitory activity of colicin K.

Authors: Matija Rijavec; Maruska Budic; Peter Mrak; Manica Müller-Premru; Zdravko Podlesek; Darja Zgur-Bertok
Journal: Appl Environ Microbiol Date: 2006-11-22 Impact factor: 4.792

Recognition of genes in DNA sequence with ambiguities.

1. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.

2. Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate.

3. Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.

4. Prevalence of ColE1-like plasmids and colicin K production among uropathogenic Escherichia coli strains and quantification of inhibitory activity of colicin K.

5. Identifying bacterial genes and endosymbiont DNA with Glimmer.

6. A markovian approach for the prediction of mouse isochores.

7. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.

8. Genome of bacteriophage P1.

9. A common virulence plasmid in biotype 2 Vibrio vulnificus and its dissemination aided by a conjugal plasmid.

Review 10. Using DNA microarrays to study host-microbe interactions.