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

Bioinformatics. 2010 Aug 15;26(16):2051-2. doi: 10.1093/bioinformatics/btq299. Epub 2010 Jun 10.

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 and plasmids, the program achieves approximately 92% in classification accuracy. On a large set of simulated metagenomes with sequence lengths ranging from 300 bp to 100 kbp, the program has classification accuracy from 64.45% to 88.75%. On a large independent test set, the program achieves 88.29% classification accuracy.

Availability: The program has been implemented as a standalone prediction program, cBar, which is available at http://csbl.bmb.uga.edu/~ffzhou/cBar.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Chromosomes / chemistry*
  • Metagenome*
  • Metagenomics / methods*
  • Plasmids / chemistry*
  • Software*