Literature DB >> 12127765

Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes.

Howard Ochman1.   

Abstract

A substantial fraction of hypothetical open reading frames (ORFs) in completely sequenced bacterial genomes are short, suggesting that many are not genes but random stretches of DNA. Although it is not feasible to authenticate the coding capacity of all such regions experimentally, comparisons of ORFs in related genomes can expose those that encode functional proteins.

Mesh：

Year:  2002        PMID： 12127765     DOI： 10.1016/s0168-9525(02)02668-9

Source DB:  PubMed          Journal:  Trends Genet        ISSN： 0168-9525            Impact factor:   11.639


  39 in total

1.  The ORFanage: an ORFan database.

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Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Identification of prokaryotic small proteins using a comparative genomic approach.

Authors:  Josue Samayoa; Fitnat H Yildiz; Kevin Karplus
Journal:  Bioinformatics       Date:  2011-05-05       Impact factor: 6.937

3.  SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes.

Authors:  Seán S Óhéigeartaigh; David Armisén; Kevin P Byrne; Kenneth H Wolfe
Journal:  J Bacteriol       Date:  2014-03-21       Impact factor: 3.490

Review 4.  Identifying (non-)coding RNAs and small peptides: challenges and opportunities.

Authors:  Andrea Pauli; Eivind Valen; Alexander F Schier
Journal:  Bioessays       Date:  2014-10-24       Impact factor: 4.345

5.  Genome-wide detection of novel regulatory RNAs in E. coli.

Authors:  Rahul Raghavan; Eduardo A Groisman; Howard Ochman
Journal:  Genome Res       Date:  2011-06-10       Impact factor: 9.043

Review 6.  Escherichia coli Small Proteome.

Authors:  Matthew R Hemm; Jeremy Weaver; Gisela Storz
Journal:  EcoSal Plus       Date:  2020-05

7.  Analysis of complete genome sequence of Neorickettsia risticii: causative agent of Potomac horse fever.

Authors:  Mingqun Lin; Chunbin Zhang; Kathryn Gibson; Yasuko Rikihisa
Journal:  Nucleic Acids Res       Date:  2009-08-06       Impact factor: 16.971

8.  Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species.

Authors:  Alejandro Caro-Quintero; Gina P Rodriguez-Castaño; Konstantinos T Konstantinidis
Journal:  J Bacteriol       Date:  2009-07-17       Impact factor: 3.490

9.  Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species.

Authors:  Hernan Lorenzi; Mathangi Thiagarajan; Brian Haas; Jennifer Wortman; Neil Hall; Elisabet Caler
Journal:  BMC Genomics       Date:  2008-12-10       Impact factor: 3.969

10.  Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.

Authors:  Wook Kim; Mark W Silby; Sam O Purvine; Julie S Nicoll; Kim K Hixson; Matt Monroe; Carrie D Nicora; Mary S Lipton; Stuart B Levy
Journal:  PLoS One       Date:  2009-12-24       Impact factor: 3.240
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