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Items: 1 to 20 of 118


Simultaneous alignment of short reads against multiple genomes.

Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

Genome Biol. 2009;10(9):R98. doi: 10.1186/gb-2009-10-9-r98. Epub 2009 Sep 17.


The Sequence Alignment/Map format and SAMtools.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.


COMPAM :visualization of combining pairwise alignments for multiple genomes.

Lee D, Choi JH, Dalkilic MM, Kim S.

Bioinformatics. 2006 Jan 15;22(2):242-4. Epub 2005 Nov 3.


Multiple whole-genome alignments without a reference organism.

Dubchak I, Poliakov A, Kislyuk A, Brudno M.

Genome Res. 2009 Apr;19(4):682-9. doi: 10.1101/gr.081778.108. Epub 2009 Jan 28.


BatMis: a fast algorithm for k-mismatch mapping.

Tennakoon C, Purbojati RW, Sung WK.

Bioinformatics. 2012 Aug 15;28(16):2122-8. doi: 10.1093/bioinformatics/bts339. Epub 2012 Jun 10.


Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.


Efficient multiple genome alignment.

Höhl M, Kurtz S, Ohlebusch E.

Bioinformatics. 2002;18 Suppl 1:S312-20.


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.


Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Brudno M, Poliakov A, Minovitsky S, Ratnere I, Dubchak I.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W669-74. Epub 2007 May 8.


Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis.

Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat JF.

J Comput Biol. 2012 Jun;19(6):796-813. doi: 10.1089/cmb.2012.0022. Epub 2012 Apr 16.


MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.

Turki T, Roshan U.

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.


SOAP2: an improved ultrafast tool for short read alignment.

Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J.

Bioinformatics. 2009 Aug 1;25(15):1966-7. doi: 10.1093/bioinformatics/btp336. Epub 2009 Jun 3.


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.


CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.

Liu Y, Schmidt B, Maskell DL.

Bioinformatics. 2012 Jul 15;28(14):1830-7. doi: 10.1093/bioinformatics/bts276. Epub 2012 May 9.


BamView: viewing mapped read alignment data in the context of the reference sequence.

Carver T, Böhme U, Otto TD, Parkhill J, Berriman M.

Bioinformatics. 2010 Mar 1;26(5):676-7. doi: 10.1093/bioinformatics/btq010. Epub 2010 Jan 12.


Multiple sequence assembly from reads alignable to a common reference genome.

Peng Q, Smith AD.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1283-95. doi: 10.1109/TCBB.2010.107.


BOAT: Basic Oligonucleotide Alignment Tool.

Zhao SQ, Wang J, Zhang L, Li JT, Gu X, Gao G, Wei L.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S2. doi: 10.1186/1471-2164-10-S3-S2.


Aligning short sequencing reads with Bowtie.

Langmead B.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32.


Sequencing of natural strains of Arabidopsis thaliana with short reads.

Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.

Genome Res. 2008 Dec;18(12):2024-33. doi: 10.1101/gr.080200.108. Epub 2008 Sep 25.


Short read alignment with populations of genomes.

Huang L, Popic V, Batzoglou S.

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.

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