TIGR gene indices clustering tools (TGICL): A software system for fast clustering of large EST datasets

Bioinformatics

Volumn 19, Issue 5, 2003, Pages 651-652

  Pertea, Geo ^a   Huang, Xiaoqiu ^b   Liang, Feng ^a,c   Antonescu, Valentin ^a   Sultana, Razvan ^a   Karamycheva, Svetlana ^a   Lee, Yuandan ^a   White, Joseph ^a   Cheung, Foo ^a   Parvizi, Babak ^a   Tsai, Jennifer ^a   Quackenbush, John ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b Iowa State University   (United States)

^c INVITROGEN CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; COMPUTER PROGRAM; CONSENSUS SEQUENCE; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENETIC ANALYSIS; GENETIC DATABASE; INFORMATION PROCESSING; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

POTATO VIRUS M;

EID: 0037460985     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg034     Document Type: Article

References (6)

1. Quackenbush,J., Cho,J., Lee,D., Liang,F., Holt,I., Karamycheva,S., Parvizi,B., Pertea,G., Sultana,R. and White,J. (2001) The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res., 29, 159-164.
2. Liang,F., Holt,I., Pertea,G., Karamycheva,S., Salzberg,S. and Quackenbush,J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res., 28, 3657-3665.
3. Chou,H.-H. and Holmes,M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics, 17:12, 1093-1104.
4. Huang,X. and Madan,A. (1999) CAP3: a DNA sequence assembly program. Genome Res., 9, 868-877.
5. Smit,AFA and Green,P. (unpublished) unpublished. See http://ftp.genome.washington.edu/cgi-bin/RepeatMasker.
6. Zhang,Z., Schwartz,S., Wagner,L. and Miller,W. (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol., 7, 203-214.