ABMapper: A suffix array-based tool for multi-location searching and splice-junction mapping

Bioinformatics

Volumn 27, Issue 3, 2011, Pages 421-422

  Lou, Shao Ke ^a   Ni, Bing ^a   Lo, Leung Yau ^a   Tsui, Stephen Kwok Wing ^a   Chan, Ting Fung ^a   Leung, Kwong Sak ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; COMPUTER PROGRAM; GENOMICS; HUMAN; METHODOLOGY; RNA SPLICING; SEQUENCE ALIGNMENT;

GENOMICS; HUMANS; RNA SPLICING; SEQUENCE ALIGNMENT; SOFTWARE; TRANSCRIPTOME;

EID: 79551588525     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq656     Document Type: Article

References (8)

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2. Au,K.F. et al. (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res., 38, 4570-4578.
3. Burrows,M. and Wheeler,D.J. (1994) A block-sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation. Palo Alto, CA.
4. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
5. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
6. Trapnell,C. et al. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
7. Wang, Z. et al. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
8. Xu,A.G. et al. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput. Biol., 6, e1000843.