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Items: 1 to 20 of 46

1.

GapMis: a tool for pairwise sequence alignment with a single gap.

Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.

Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.

PMID:
22974258
2.

libgapmis: extending short-read alignments.

Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.

BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.

3.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

4.

CGAP-align: a high performance DNA short read alignment tool.

Chen Y, Hong J, Cui W, Zaneveld J, Wang W, Gibbs R, Xiao Y, Chen R.

PLoS One. 2013 Apr 11;8(4):e61033. doi: 10.1371/journal.pone.0061033. Print 2013.

5.

Error tolerant indexing and alignment of short reads with covering template families.

Giladi E, Healy J, Myers G, Hart C, Kapranov P, Lipson D, Roels S, Thayer E, Letovsky S.

J Comput Biol. 2010 Oct;17(10):1397-1411. doi: 10.1089/cmb.2010.0005.

PMID:
20937014
6.

GASSST: global alignment short sequence search tool.

Rizk G, Lavenier D.

Bioinformatics. 2010 Oct 15;26(20):2534-40. doi: 10.1093/bioinformatics/btq485. Epub 2010 Aug 24.

7.

BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data.

Larsen PE, Collart FR.

BMC Res Notes. 2012 Jun 7;5:275. doi: 10.1186/1756-0500-5-275.

8.

Short read mapping for exome sequencing.

Zhou X, Bao S, Wang B, Zhang X, Song YQ.

Methods Mol Biol. 2013;1038:93-111. doi: 10.1007/978-1-62703-514-9_6.

PMID:
23872971
9.

On global sequence alignment.

Huang X.

Comput Appl Biosci. 1994 Jun;10(3):227-35.

PMID:
7922677
10.

GenomeView: a next-generation genome browser.

Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y.

Nucleic Acids Res. 2012 Jan;40(2):e12. doi: 10.1093/nar/gkr995. Epub 2011 Nov 18.

11.
12.

Short read DNA fragment anchoring algorithm.

Wang W, Zhang P, Liu X.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S17. doi: 10.1186/1471-2105-10-S1-S17.

13.

Adaptive Smith-Waterman residue match seeding for protein structural alignment.

Topham CM, Rouquier M, Tarrat N, André I.

Proteins. 2013 Oct;81(10):1823-39. doi: 10.1002/prot.24327. Epub 2013 Aug 19.

PMID:
23720362
14.

A genetic algorithm for multiple molecular sequence alignment.

Zhang C, Wong AK.

Comput Appl Biosci. 1997 Dec;13(6):565-81.

PMID:
9475984
15.

SRmapper: a fast and sensitive genome-hashing alignment tool.

Gontarz PM, Berger J, Wong CF.

Bioinformatics. 2013 Feb 1;29(3):316-21. doi: 10.1093/bioinformatics/bts712. Epub 2012 Dec 24.

PMID:
23267171
16.

Analysis of high-throughput sequencing data.

Mane SP, Modise T, Sobral BW.

Methods Mol Biol. 2011;678:1-11. doi: 10.1007/978-1-60761-682-5_1.

PMID:
20931368
17.

Multiple sequence alignment using simulated annealing.

Kim J, Pramanik S, Chung MJ.

Comput Appl Biosci. 1994 Jul;10(4):419-26.

PMID:
7804875
18.

Murlet: a practical multiple alignment tool for structural RNA sequences.

Kiryu H, Tabei Y, Kin T, Asai K.

Bioinformatics. 2007 Jul 1;23(13):1588-98. Epub 2007 Apr 25.

PMID:
17459961
19.

Co-phylog: an assembly-free phylogenomic approach for closely related organisms.

Yi H, Jin L.

Nucleic Acids Res. 2013 Apr;41(7):e75. doi: 10.1093/nar/gkt003. Epub 2013 Jan 18.

20.

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.

Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I.

Bioinformatics. 2008 Jul 1;24(13):i32-40. doi: 10.1093/bioinformatics/btn173.

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