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Items: 17

1.

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

Chen Q, Zobel J, Verspoor K.

Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw163. Print 2017.

2.

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.

Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH; UniProt Consortium.

Bioinformatics. 2015 Mar 15;31(6):926-32. doi: 10.1093/bioinformatics/btu739. Epub 2014 Nov 13.

3.

nDNA-Prot: identification of DNA-binding proteins based on unbalanced classification.

Song L, Li D, Zeng X, Wu Y, Guo L, Zou Q.

BMC Bioinformatics. 2014 Sep 8;15:298. doi: 10.1186/1471-2105-15-298.

4.

kClust: fast and sensitive clustering of large protein sequence databases.

Hauser M, Mayer CE, Söding J.

BMC Bioinformatics. 2013 Aug 15;14:248. doi: 10.1186/1471-2105-14-248.

5.

First comparative transcriptomic analysis of wild adult male and female Lutzomyia longipalpis, vector of visceral leishmaniasis.

McCarthy CB, Santini MS, Pimenta PF, Diambra LA.

PLoS One. 2013;8(3):e58645. doi: 10.1371/journal.pone.0058645. Epub 2013 Mar 12.

6.

Ultrafast clustering algorithms for metagenomic sequence analysis.

Li W, Fu L, Niu B, Wu S, Wooley J.

Brief Bioinform. 2012 Nov;13(6):656-68. doi: 10.1093/bib/bbs035. Epub 2012 Jul 6.

7.

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.

Gahlan P, Singh HR, Shankar R, Sharma N, Kumari A, Chawla V, Ahuja PS, Kumar S.

BMC Genomics. 2012 Mar 31;13:126. doi: 10.1186/1471-2164-13-126.

8.

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.

BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.

9.

Metagenomic analysis of taxa associated with Lutzomyia longipalpis, vector of visceral leishmaniasis, using an unbiased high-throughput approach.

McCarthy CB, Diambra LA, Rivera Pomar RV.

PLoS Negl Trop Dis. 2011 Sep;5(9):e1304. doi: 10.1371/journal.pntd.0001304. Epub 2011 Sep 6.

10.

PSI-2: structural genomics to cover protein domain family space.

Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C.

Structure. 2009 Jun 10;17(6):869-81. doi: 10.1016/j.str.2009.03.015. Review.

11.

Probing metagenomics by rapid cluster analysis of very large datasets.

Li W, Wooley JC, Godzik A.

PLoS One. 2008;3(10):e3375. doi: 10.1371/journal.pone.0003375. Epub 2008 Oct 10.

12.
13.

FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB.

Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Mølgaard A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W84-8.

14.

HHsenser: exhaustive transitive profile search using HMM-HMM comparison.

Söding J, Remmert M, Biegert A, Lupas AN.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W374-8.

15.

Wiggle-predicting functionally flexible regions from primary sequence.

Gu J, Gribskov M, Bourne PE.

PLoS Comput Biol. 2006 Jul 14;2(7):e90. Epub 2006 Jun 5.

16.

Intrinsic disorder in transcription factors.

Liu J, Perumal NB, Oldfield CJ, Su EW, Uversky VN, Dunker AK.

Biochemistry. 2006 Jun 6;45(22):6873-88.

17.

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