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Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes

Paper ID Volume ID Publish Year Pages File Format Full-Text
15502 1419 2006 15 PDF Available
Title
Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes
Abstract

We developed a statistical method that allows each trinucleotide to be associated with a unique frame among the three possible ones in a (protein coding) gene. An extensive gene study in 175 complete bacterial genomes based on this statistical approach resulted in identification of 72 new circular codes. Finding a circular code enables an immediate retrieval of the reading frame locally anywhere in a gene. No knowledge of location of the start codon is required and a short window of only a few nucleotides is sufficient for automatic retrieval. We have therefore developed a factorization method (that explores previously found circular codes) for retrieving the reading frames of bacterial genes. Its principle is new and easy to understand. Neither complex treatment nor specific information on the nucleotide sequences is necessary. Moreover, the method can be used for short regions in nucleotide sequences (less than 25 nucleotides in protein coding genes). Selected additional properties of circular codes and their possible biological consequences are also discussed.

Keywords
Bacterial genome; Circular code; Frame
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Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 30, Issue 2, April 2006, Pages 87–101
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
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