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Items: 1 to 20 of 98

1.

Simrank: Rapid and sensitive general-purpose k-mer search tool.

DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N.

BMC Ecol. 2011 Apr 27;11:11. doi: 10.1186/1472-6785-11-11.

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PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.

Li A, Zhang J, Zhou Z.

BMC Bioinformatics. 2014 Sep 19;15:311. doi: 10.1186/1471-2105-15-311.

4.

Optimizing Spaced k-mer Neighbors for Efficient Filtration in Protein Similarity Search.

Li W, Ma B, Zhang K.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Mar-Apr;11(2):398-406. doi: 10.1109/TCBB.2014.2306831.

PMID:
26355786
5.

PTPan--overcoming memory limitations in oligonucleotide string matching for primer/probe design.

Eissler T, Hodges CP, Meier H.

Bioinformatics. 2011 Oct 15;27(20):2797-805. doi: 10.1093/bioinformatics/btr483. Epub 2011 Aug 19.

PMID:
21856736
6.

SSAHA: a fast search method for large DNA databases.

Ning Z, Cox AJ, Mullikin JC.

Genome Res. 2001 Oct;11(10):1725-9.

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Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes.

Cummings L, Riley L, Black L, Souvorov A, Resenchuk S, Dondoshansky I, Tatusova T.

FEMS Microbiol Lett. 2002 Nov 5;216(2):133-8.

10.

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

Kurtz S, Narechania A, Stein JC, Ware D.

BMC Genomics. 2008 Oct 31;9:517. doi: 10.1186/1471-2164-9-517.

11.

Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology.

Li W, Pio F, Pawłowski K, Godzik A.

Bioinformatics. 2000 Dec;16(12):1105-10.

PMID:
11159329
12.

Rapid similarity search of proteins using alignments of domain arrangements.

Terrapon N, Weiner J, Grath S, Moore AD, Bornberg-Bauer E.

Bioinformatics. 2014 Jan 15;30(2):274-81. doi: 10.1093/bioinformatics/btt379. Epub 2013 Jul 4.

PMID:
23828785
13.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

14.

Re-searcher: a system for recurrent detection of homologous protein sequences.

Repsys V, Margelevicius M, Venclovas C.

BMC Bioinformatics. 2008 Jun 27;9:296. doi: 10.1186/1471-2105-9-296.

15.

WindowMasker: window-based masker for sequenced genomes.

Morgulis A, Gertz EM, Schäffer AA, Agarwala R.

Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.

PMID:
16287941
16.

FastBLAST: homology relationships for millions of proteins.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2008;3(10):e3589. doi: 10.1371/journal.pone.0003589. Epub 2008 Oct 31.

17.

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

Teichert F, Minning J, Bastolla U, Porto M.

BMC Bioinformatics. 2010 May 14;11:251. doi: 10.1186/1471-2105-11-251.

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SSMAL: similarity searching with alignment graphs.

Nicodème P.

Bioinformatics. 1998;14(6):508-15.

PMID:
9694989
20.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA.

BMC Bioinformatics. 2010 Jun 12;11:317. doi: 10.1186/1471-2105-11-317.

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