Literature DB >> 20436475

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.

Amrita Pati1, Natalia N Ivanova, Natalia Mikhailova, Galina Ovchinnikova, Sean D Hooper, Athanasios Lykidis, Nikos C Kyrpides.   

Abstract

We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.

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Year:  2010        PMID： 20436475     DOI： 10.1038/nmeth.1457

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  14 in total

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2.  Identifying bacterial genes and endosymbiont DNA with Glimmer.

Authors:  Arthur L Delcher; Kirsten A Bratke; Edwin C Powers; Steven L Salzberg
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3.  Mass spectrometry-based prokaryote gene annotation.

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4.  Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream.

Authors:  Nikos C Kyrpides
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5.  Accuracy improvement for identifying translation initiation sites in microbial genomes.

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Journal:  Bioinformatics       Date:  2004-07-09       Impact factor: 6.937

6.  Discovery and revision of Arabidopsis genes by proteogenomics.

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7.  GenBank.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2009-11-12       Impact factor: 16.971

8.  Experimental determination of translational start sites resolves uncertainties in genomic open reading frame predictions - application to Mycobacterium tuberculosis.

Authors:  Katherine L Smollett; Amanda S Fivian-Hughes; Joanne E Smith; Anchi Chang; Tara Rao; Elaine O Davis
Journal:  Microbiology (Reading)       Date:  2009-01       Impact factor: 2.777

9.  An unsupervised classification scheme for improving predictions of prokaryotic TIS.

Authors:  Maike Tech; Peter Meinicke
Journal:  BMC Bioinformatics       Date:  2006-03-09       Impact factor: 3.169

10.  A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

Authors:  G X Yu; E E Snyder; S M Boyle; O R Crasta; M Czar; S P Mane; A Purkayastha; B Sobral; J C Setubal
Journal:  Nucleic Acids Res       Date:  2007-06-06       Impact factor: 16.971
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  413 in total

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Journal:  J Bacteriol       Date:  2011-12       Impact factor: 3.490

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Authors:  Kathryne G Byrne-Bailey; John D Coates
Journal:  J Bacteriol       Date:  2012-05       Impact factor: 3.490

3.  Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete.

Authors:  Jennifer R Davis; Lynne A Goodwin; Tanja Woyke; Hazuki Teshima; David Bruce; Chris Detter; Roxanne Tapia; Shunsheng Han; James Han; Sam Pitluck; Matt Nolan; Natalia Mikhailova; Miriam L Land; Jason K Sello
Journal:  J Bacteriol       Date:  2012-05       Impact factor: 3.490

4.  Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198.

Authors:  Konstantinos Papadimitriou; Stéphanie Ferreira; Nikolaos C Papandreou; Eleni Mavrogonatou; Philip Supply; Bruno Pot; Effie Tsakalidou
Journal:  J Bacteriol       Date:  2012-04       Impact factor: 3.490

5.  Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil.

Authors:  Robert J Martinez; David Bruce; Chris Detter; Lynne A Goodwin; James Han; Cliff S Han; Brittany Held; Miriam L Land; Natalia Mikhailova; Matt Nolan; Len Pennacchio; Sam Pitluck; Roxanne Tapia; Tanja Woyke; Patricia A Sobecky
Journal:  J Bacteriol       Date:  2012-04       Impact factor: 3.490

6.  DNA-energetics-based analyses suggest additional genes in prokaryotes.

Authors:  Garima Khandelwal; Jalaj Gupta; B Jayaram
Journal:  J Biosci       Date:  2012-07       Impact factor: 1.826

7.  Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass.

Authors:  Sara E Blumer-Schuette; Richard J Giannone; Jeffrey V Zurawski; Inci Ozdemir; Qin Ma; Yanbin Yin; Ying Xu; Irina Kataeva; Farris L Poole; Michael W W Adams; Scott D Hamilton-Brehm; James G Elkins; Frank W Larimer; Miriam L Land; Loren J Hauser; Robert W Cottingham; Robert L Hettich; Robert M Kelly
Journal:  J Bacteriol       Date:  2012-05-25       Impact factor: 3.490

8.  High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes.

Authors:  Jantiya Isanapong; Lynne Goodwin; David Bruce; Amy Chen; Chris Detter; James Han; Cliff S Han; Brittany Held; Marcel Huntemann; Natalia Ivanova; Miriam L Land; Konstantinos Mavromatis; Matt Nolan; Amrita Pati; Len Pennacchio; Sam Pitluck; Ernest Szeto; Roxanne Tapia; Tanja Woyke; Jorge L M Rodrigues
Journal:  J Bacteriol       Date:  2012-05       Impact factor: 3.490

9.  Complete genome sequence of Rahnella aquatilis CIP 78.65.

Authors:  Robert J Martinez; David Bruce; Chris Detter; Lynne A Goodwin; James Han; Cliff S Han; Brittany Held; Miriam L Land; Natalia Mikhailova; Matt Nolan; Len Pennacchio; Sam Pitluck; Roxanne Tapia; Tanja Woyke; Patricia A Sobecky
Journal:  J Bacteriol       Date:  2012-06       Impact factor: 3.490

10.  Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia.

Authors:  Dwi Susanti; Eric F Johnson; Jason R Rodriguez; Iain Anderson; Anna A Perevalova; Nikos Kyrpides; Susan Lucas; James Han; Alla Lapidus; Jan-Fang Cheng; Lynne Goodwin; Sam Pitluck; Konstantinos Mavrommatis; Lin Peters; Miriam L Land; Loren Hauser; Venkat Gopalan; Patricia P Chan; Todd M Lowe; Haruyuki Atomi; Elizaveta A Bonch-Osmolovskaya; Tanja Woyke; Biswarup Mukhopadhyay
Journal:  J Bacteriol       Date:  2012-10       Impact factor: 3.490
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