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Items: 1 to 20 of 143

1.

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information.

Konwar KM, Hanson NW, Pagé AP, Hallam SJ.

BMC Bioinformatics. 2013 Jun 21;14:202. doi: 10.1186/1471-2105-14-202.

2.

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

Konwar KM, Hanson NW, Bhatia MP, Kim D, Wu SJ, Hahn AS, Morgan-Lang C, Cheung HK, Hallam SJ.

Bioinformatics. 2015 Oct 15;31(20):3345-7. doi: 10.1093/bioinformatics/btv361.

3.

Metabolic pathways for the whole community.

Hanson NW, Konwar KM, Hawley AK, Altman T, Karp PD, Hallam SJ.

BMC Genomics. 2014 Jul 22;15:619. doi: 10.1186/1471-2164-15-619.

4.
5.

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X.

BMC Genomics. 2012 Dec 20;13:715. doi: 10.1186/1471-2164-13-715.

6.

TaxMan: a taxonomic database manager.

Jones M, Blaxter M.

BMC Bioinformatics. 2006 Dec 18;7:536.

7.

GFF-Ex: a genome feature extraction package.

Rastogi A, Gupta D.

BMC Res Notes. 2014 May 24;7:315. doi: 10.1186/1756-0500-7-315.

8.

ESTIMA, a tool for EST management in a multi-project environment.

Kumar CG, LeDuc R, Gong G, Roinishivili L, Lewin HA, Liu L.

BMC Bioinformatics. 2004 Nov 4;5:176.

9.

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

Database (Oxford). 2011 Apr 7;2011:bar008. doi: 10.1093/database/bar008.

10.

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.

11.

AutoFACT: an automatic functional annotation and classification tool.

Koski LB, Gray MW, Lang BF, Burger G.

BMC Bioinformatics. 2005 Jun 16;6:151.

12.

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA.

BMC Bioinformatics. 2008 Sep 19;9:386. doi: 10.1186/1471-2105-9-386.

13.

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE, Main D.

Database (Oxford). 2013 Oct 25;2013:bat075. doi: 10.1093/database/bat075.

14.

PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences.

Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.

Bioinformatics. 2007 Apr 1;23(7):793-801.

15.

G-InforBIO: integrated system for microbial genomics.

Tanaka N, Abe T, Miyazaki S, Sugawara H.

BMC Bioinformatics. 2006 Aug 4;7:368.

16.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Kuhn A, Luthi-Carter R, Delorenzi M.

BMC Bioinformatics. 2008 Jan 17;9:26. doi: 10.1186/1471-2105-9-26.

17.

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A.

Bioinformatics. 2005 Jun 15;21(12):2814-20.

18.

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes.

Wylie T, Martin J, Abubucker S, Yin Y, Messina D, Wang Z, McCarter JP, Mitreva M.

BMC Genomics. 2008 Nov 4;9:525. doi: 10.1186/1471-2164-9-525.

19.

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.

Feng X, Xu Y, Chen Y, Tang YJ.

BMC Syst Biol. 2012 Aug 2;6:94.

20.

FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.

Paschall JE, Oleksiak MF, VanWye JD, Roach JL, Whitehead JA, Wyckoff GJ, Kolell KJ, Crawford DL.

BMC Genomics. 2004 Dec 20;5(1):96.

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