AUTOMATIC ANNOTATION OF BACTERIAL COMMUNITY SEQUENCES AND APPLICATION TO INFECTIONS DIAGNOSTIC

Victor Solovyev, Asaf Salamov, Igor Seledtsov, Denis Vorobyev, Alexander Bachinsky

2011

Abstract

To annotate bacterial sequences from an environmental sample, we have developed an automatic annotation pipeline Fgenesb_annotator that includes self-training of gene-finding parameters, prediction of CDS, RNA genes, operons, promoters and terminators. New version of pipeline includes frame shift corrections and special module with improved prediction accuracy of ribosomal proteins. To analyze next-generation sequencing data we have developed OligiZip assembler and Transomics pipeline that provide solutions to the following tasks: 1) de novo reconstruction of genomic sequence; 2) reconstruction of sequence with a reference genome; 3) SNP discovery; 4) mapping RNA-Seq data to a reference genome, assemble them into alternative transcripts and quantify the abundance of these transcripts. Using the OligoZip assembler and gene Fgenesb pipeline we have developed a novel computational approach of identification toxic and non-toxic bacterial serotypes using next-generation sequencing data. It can be used for detection of bacterial infections in wounds, water or food contamination.

Paper Citation

in Harvard Style

Solovyev V., Salamov A., Seledtsov I., Vorobyev D. and Bachinsky A. (2011). AUTOMATIC ANNOTATION OF BACTERIAL COMMUNITY SEQUENCES AND APPLICATION TO INFECTIONS DIAGNOSTIC . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: Meta, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 346-353. DOI: 10.5220/0003333703460353

in Bibtex Style

@conference{meta11,
author={Victor Solovyev and Asaf Salamov and Igor Seledtsov and Denis Vorobyev and Alexander Bachinsky},
title={AUTOMATIC ANNOTATION OF BACTERIAL COMMUNITY SEQUENCES AND APPLICATION TO INFECTIONS DIAGNOSTIC},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: Meta, (BIOSTEC 2011)},
year={2011},
pages={346-353},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003333703460353},
isbn={978-989-8425-36-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: Meta, (BIOSTEC 2011)
TI - AUTOMATIC ANNOTATION OF BACTERIAL COMMUNITY SEQUENCES AND APPLICATION TO INFECTIONS DIAGNOSTIC
SN - 978-989-8425-36-2
AU - Solovyev V.
AU - Salamov A.
AU - Seledtsov I.
AU - Vorobyev D.
AU - Bachinsky A.
PY - 2011
SP - 346
EP - 353
DO - 10.5220/0003333703460353