loading
Papers

Research.Publish.Connect.

Paper

Paper Unlock

Authors: Victor Solovyev 1 ; Asaf Salamov 2 ; Igor Seledtsov 2 ; Denis Vorobyev 3 and Alexander Bachinsky 4

Affiliations: 1 Royal Holloway and University of London, United Kingdom ; 2 Softberry Inc., United States ; 3 Softbery Inc., United States ; 4 Softberry. Inc., United States

ISBN: 978-989-8425-36-2

Keyword(s): Bacterial community, Genome annotation, Sequence assembling, RNA-seq data, Computational pipelines, classification and diagnostic pathogenic bacteria, Tanscriptome analysis.

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. (More)

PDF ImageFull Text

Download
CC BY-NC-ND 4.0

Sign In Guest: Register as new SciTePress user now for free.

Sign In SciTePress user: please login.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 3.227.249.234

In the current month:
Recent papers: 100 available of 100 total
2+ years older papers: 200 available of 200 total

Paper citation in several formats:
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

@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},
}

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

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.