Projector 2: Contig Mapping for Efficient Gap-closure of Prokaryotic Genome Sequence Assemblies

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Jun 28

PMID 15980536

Citations 47

Authors

Sacha A F T van Hijum

Aldert L Zomer

Oscar P Kuipers

Jan Kok

Affiliations

Soon will be listed here.

Abstract

With genome sequencing efforts increasing exponentially, valuable information accumulates on genomic content of the various organisms sequenced. Projector 2 uses (un)finished genomic sequences of an organism as a template to infer linkage information for a genome sequence assembly of a related organism being sequenced. The remaining gaps between contigs for which no linkage information is present can subsequently be closed with direct PCR strategies. Compared with other implementations, Projector 2 has several distinctive features: a user-friendly web interface, automatic removal of repetitive elements (repeat-masking) and automated primer design for gap-closure purposes. Moreover, when using multiple fragments of a template genome, primers for multiplex PCR strategies can also be designed. Primer design takes into account that, in many cases, contig ends contain unreliable DNA sequences and repetitive sequences. Closing the remaining gaps in prokaryotic genome sequence assemblies is thereby made very efficient and virtually effortless. We demonstrate that the use of single or multiple fragments of a template genome (i.e. unfinished genome sequences) in combination with repeat-masking results in mapping success rates close to 100%. The web interface is freely accessible at http://molgen.biol.rug.nl/websoftware/projector2.

Citing Articles

Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements.

Chen K, Shen H, Lu C BMC Syst Biol. 2019; 12(Suppl 9):139.

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Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate.

Ziesack M, Karrenbelt M, Bues J, Schaefer E, Silver P, Way J Microbiol Resour Announc. 2018; 7(22).

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Genomics-guided discovery of a new and significantly better source of anticancer natural drug FK228.

Liu X, Xie F, Doughty L, Wang Q, Zhang L, Liu X Synth Syst Biotechnol. 2018; 3(4):268-274.

PMID: 30417143 PMC: 6222137. DOI: 10.1016/j.synbio.2018.10.011.

CSAR-web: a web server of contig scaffolding using algebraic rearrangements.

Chen K, Lu C Nucleic Acids Res. 2018; 46(W1):W55-W59.

PMID: 29733393 PMC: 6030906. DOI: 10.1093/nar/gky337.

Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis.

Singh P, Chung H, Lee I, DSouza R, Kim H, Hong S BMC Genomics. 2018; 19(1):292.

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