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Results: 1 to 20 of 57

1.

The need for speed.

Flicek P.

Genome Biol. 2009;10(3):212. doi: 10.1186/gb-2009-10-3-212. Epub 2009 Mar 27.

PMID:
19344490
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Fast gapped-read alignment with Bowtie 2.

Langmead B, Salzberg SL.

Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.

PMID:
22388286
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

PMID:
19261174
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

THOR: targeted high-throughput ortholog reconstructor.

Bainbridge MN, Warren RL, He A, Bilenky M, Robertson AG, Jones SJ.

Bioinformatics. 2007 Oct 1;23(19):2622-4. Epub 2006 Oct 11.

PMID:
17038343
[PubMed - indexed for MEDLINE]
Free Article
5.

Compressed indexing and local alignment of DNA.

Lam TW, Sung WK, Tam SL, Wong CK, Yiu SM.

Bioinformatics. 2008 Mar 15;24(6):791-7. doi: 10.1093/bioinformatics/btn032. Epub 2008 Jan 28.

PMID:
18227115
[PubMed - indexed for MEDLINE]
Free Article
6.

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles.

Abeel T, Saeys Y, Rouzé P, Van de Peer Y.

Bioinformatics. 2008 Jul 1;24(13):i24-31. doi: 10.1093/bioinformatics/btn172.

PMID:
18586720
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A fast and sensitive algorithm for aligning ESTs to the human genome.

Ogasawara J, Morishita S.

J Bioinform Comput Biol. 2003 Jul;1(2):363-86.

PMID:
15303288
[PubMed - indexed for MEDLINE]
8.

Decomposition of overlapping patterns by cumulative local cross-correlation.

Kogan SB.

J Bioinform Comput Biol. 2006 Apr;4(2):571-87.

PMID:
16819803
[PubMed - indexed for MEDLINE]
9.

Space-conserving optimal DNA-protein alignment.

Ko P, Narayanan M, Kalyanaraman A, Aluru S.

Proc IEEE Comput Syst Bioinform Conf. 2004:80-8.

PMID:
16448002
[PubMed - indexed for MEDLINE]
10.

Homology assessment and molecular sequence alignment.

Phillips AJ.

J Biomed Inform. 2006 Feb;39(1):18-33. Epub 2005 Dec 9. Review.

PMID:
16380300
[PubMed - indexed for MEDLINE]
Free Article
11.

Segmentation algorithm for DNA sequences.

Zhang CT, Gao F, Zhang R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Oct;72(4 Pt 1):041917. Epub 2005 Oct 17.

PMID:
16383430
[PubMed - indexed for MEDLINE]
12.

Antisense starts making more sense.

Carmichael GG.

Nat Biotechnol. 2003 Apr;21(4):371-2. No abstract available.

PMID:
12665819
[PubMed - indexed for MEDLINE]
13.

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.

PMID:
16542424
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Local alignment of two-base encoded DNA sequence.

Homer N, Merriman B, Nelson SF.

BMC Bioinformatics. 2009 Jun 9;10:175. doi: 10.1186/1471-2105-10-175.

PMID:
19508732
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases.

Miller C, Gurd J, Brass A.

Bioinformatics. 1999 Feb;15(2):111-21.

PMID:
10089196
[PubMed - indexed for MEDLINE]
Free Article
16.

Design and assessment of a fast algorithm for identifying specific probes for human and mouse genes.

Chang PC, Peck K.

Bioinformatics. 2003 Jul 22;19(11):1311-7.

PMID:
12874041
[PubMed - indexed for MEDLINE]
Free Article
17.

CSA: an efficient algorithm to improve circular DNA multiple alignment.

Fernandes F, Pereira L, Freitas AT.

BMC Bioinformatics. 2009 Jul 23;10:230. doi: 10.1186/1471-2105-10-230.

PMID:
19627599
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Constructing near-perfect phylogenies with multiple homoplasy events.

Satya RV, Mukherjee A, Alexe G, Parida L, Bhanot G.

Bioinformatics. 2006 Jul 15;22(14):e514-22.

PMID:
16873515
[PubMed - indexed for MEDLINE]
Free Article
19.

Consensus generation and variant detection by Celera Assembler.

Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G.

Bioinformatics. 2008 Apr 15;24(8):1035-40. doi: 10.1093/bioinformatics/btn074. Epub 2008 Mar 4.

PMID:
18321888
[PubMed - indexed for MEDLINE]
Free Article
20.

Widespread occurrence of antisense transcription in the human genome.

Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, Nemzer S, Pinner E, Walach S, Bernstein J, Savitsky K, Rotman G.

Nat Biotechnol. 2003 Apr;21(4):379-86. Epub 2003 Mar 17.

PMID:
12640466
[PubMed - indexed for MEDLINE]

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