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Items: 1 to 20 of 96

1.

Identifying bacterial genes and endosymbiont DNA with Glimmer.

Delcher AL, Bratke KA, Powers EC, Salzberg SL.

Bioinformatics. 2007 Mar 15;23(6):673-9. Epub 2007 Jan 19.

2.

Comprehensive DNA signature discovery and validation.

Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL.

PLoS Comput Biol. 2007 May;3(5):e98. Epub 2007 Apr 20.

3.

Accuracy improvement for identifying translation initiation sites in microbial genomes.

Zhu HQ, Hu GQ, Ouyang ZQ, Wang J, She ZS.

Bioinformatics. 2004 Dec 12;20(18):3308-17. Epub 2004 Jul 9.

PMID:
15247104
4.

Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont.

Foster JM, Kumar S, Ganatra MB, Kamal IH, Ware J, Ingram J, Pope-Chappell J, Guiliano D, Whitton C, Daub J, Blaxter ML, Slatko BE.

Int J Parasitol. 2004 May;34(6):733-46.

PMID:
15111095
5.

Microbial gene identification using interpolated Markov models.

Salzberg SL, Delcher AL, Kasif S, White O.

Nucleic Acids Res. 1998 Jan 15;26(2):544-8.

6.

Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes.

Shmatkov AM, Melikyan AA, Chernousko FL, Borodovsky M.

Bioinformatics. 1999 Nov;15(11):874-86.

PMID:
10743554
7.

Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella.

Schmidt EW, Nelson JT, Rasko DA, Sudek S, Eisen JA, Haygood MG, Ravel J.

Proc Natl Acad Sci U S A. 2005 May 17;102(20):7315-20. Epub 2005 May 9.

8.

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.

Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):E1423-32. doi: 10.1073/pnas.1111712108. Epub 2011 Nov 28.

9.

Scaffolding and validation of bacterial genome assemblies using optical restriction maps.

Nagarajan N, Read TD, Pop M.

Bioinformatics. 2008 May 15;24(10):1229-35. doi: 10.1093/bioinformatics/btn102. Epub 2008 Mar 20.

10.

Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER.

Aggarwal G, Ramaswamy R.

J Biosci. 2002 Feb;27(1 Suppl 1):7-14.

11.

Finding novel genes in bacterial communities isolated from the environment.

Krause L, Diaz NN, Bartels D, Edwards RA, Pühler A, Rohwer F, Meyer F, Stoye J.

Bioinformatics. 2006 Jul 15;22(14):e281-9.

PMID:
16873483
12.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

Powell BC, Hutchison CA 3rd.

BMC Bioinformatics. 2006 Jan 19;7:31.

13.

Prokaryotic gene prediction using GeneMark and GeneMark.hmm.

Borodovsky M, Mills R, Besemer J, Lomsadze A.

Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.5. doi: 10.1002/0471250953.bi0405s01.

PMID:
18428700
14.

Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures.

Dalevi D, Dubhashi D, Hermansson M.

Bioinformatics. 2006 Mar 1;22(5):517-22. Epub 2006 Jan 10.

PMID:
16403797
15.

CONSORF: a consensus prediction system for prokaryotic coding sequences.

Kang S, Yang SJ, Kim S, Bhak J.

Bioinformatics. 2007 Nov 15;23(22):3088-90. Epub 2007 Oct 31.

PMID:
17977885
16.

Development of joint application strategies for two microbial gene finders.

McHardy AC, Goesmann A, Pühler A, Meyer F.

Bioinformatics. 2004 Jul 10;20(10):1622-31. Epub 2004 Feb 26.

PMID:
14988122
17.

Genome streamlining and chemical defense in a coral reef symbiosis.

Kwan JC, Donia MS, Han AW, Hirose E, Haygood MG, Schmidt EW.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20655-60. doi: 10.1073/pnas.1213820109. Epub 2012 Nov 26.

19.

PREDetector: a new tool to identify regulatory elements in bacterial genomes.

Hiard S, Marée R, Colson S, Hoskisson PA, Titgemeyer F, van Wezel GP, Joris B, Wehenkel L, Rigali S.

Biochem Biophys Res Commun. 2007 Jun 15;357(4):861-4. Epub 2007 Apr 12.

20.

Eukaryotic gene prediction using GeneMark.hmm.

Borodovsky M, Lomsadze A, Ivanov N, Mills R.

Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.6. doi: 10.1002/0471250953.bi0406s01.

PMID:
18428701

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