CBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.

ABSTRACT:

Summary

Huge amount of metagenomic sequence data have been produced as a result of the rapidly increasing efforts worldwide in studying microbial communities as a whole. Most, if not all, sequenced metagenomes are complex mixtures of chromosomal and plasmid sequence fragments from multiple organisms, possibly from different kingdoms. Computational methods for prediction of genomic elements such as genes are significantly different for chromosomes and plasmids, hence raising the need for separation of chromosomal from plasmid sequences in a metagenome. We present a program for classification of a metagenome set into chromosomal and plasmid sequences, based on their distinguishing pentamer frequencies. On a large training set consisting of all the sequenced prokaryotic chromosomes an

SUBMITTER: Zhou F 

PROVIDER: S-EPMC2916713 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature