ArticleNucleic acids research2005
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements.BMC systems biology · 2018Article
- Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate.Microbiology resource announcements · 2018Article
- Genomics-guided discovery of a new and significantly better source of anticancer natural drug FK228.Synthetic and systems biotechnology · 2018Article
- CSAR-web: a web server of contig scaffolding using algebraic rearrangements.Nucleic acids research · 2018Article
- Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis.BMC genomics · 2018Article
- IndigenousFrontiers in microbiology · 2018Article
- A New Resistance Gene against Potato Late Blight Originating fromFrontiers in plant science · 2017Article
- Complete Genome Sequencing ofFrontiers in microbiology · 2017Article
- Metagenomic Assembly: Overview, Challenges and Applications.The Yale journal of biology and medicine · 2016Review
- Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences.GigaScience · 2016Article
- Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.Pharmaceutics · 2016Review
- Microbial bioinformatics for food safety and production.Briefings in bioinformatics · 2016Review
- Draft Genome Sequence of Ochrobactrum anthropi Strain ML7 Isolated from Soil Samples in Vinhphuc Province, Vietnam.Genome announcements · 2015Article
- Molecular mechanism of nicotine degradation by a newly isolated strain, Ochrobactrum sp. strain SJY1.Applied and environmental microbiology · 2015Article
- An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches.Microbes and environments · 2015Article
- CAR: contig assembly of prokaryotic draft genomes using rearrangements.BMC bioinformatics · 2014Article
- Perfrin, a novel bacteriocin associated with netB positive Clostridium perfringens strains from broilers with necrotic enteritis.Veterinary research · 2014Article
- Article
- Combining de novo and reference-guided assembly with scaffold_builder.Source code for biology and medicine · 2013Article
- Complete Genome Sequence of the Probiotic Bifidobacterium thermophilum Strain RBL67.Genome announcements · 2013Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.