The TIGR Gene Indices: Clustering and assembling EST and know genes and integration with eukaryotic genomes

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Lee, Y ^a   Tsai, J ^a   Sunkara, S ^a   Karamycheva, S ^a   Pertea, G ^a   Sultana, R ^a   Antonescu, V ^a   Chan, A ^a   Cheung, F ^a   Quackenbush, J ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE GENE MAPPING; COMPUTER INTERFACE; COMPUTER PROGRAM; EUKARYOTE; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC TRANSCRIPTION; HUMAN; INTERNET; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SPECIES DIVERSITY; TIGR GENE INDEX; BIOINFORMATICS; FUNCTIONAL GENOMICS; GENE MAPPING; GENOMICS; OPEN READING FRAME; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; CONSENSUS SEQUENCE; DATABASES, GENETIC; EUKARYOTIC CELLS; EXPRESSED SEQUENCE TAGS; GENOME; GENOMICS; HUMANS; INTERNET; SEQUENCE ANALYSIS, DNA; SOFTWARE;

COMPLEMENTARY DNA;

EUKARYOTA;

EID: 13444273452     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki064     Document Type: Article

References (11)

1. Quackenbush,J., Liang,F., Holt,I., Pertea,G. and Upton,J. (2000) The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res., 28, 141-145.
2. 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.
3. Liang,F., Holt,I., Pertea,G., Karamycheva,S., Salzberg,S.L. and Quackenbush,J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res., 28, 3657-3665.
4. Zhang,Z., Schwartz,S., Wagner,L. and Miller,W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7 203-214.
5. Huang,X. and Madan,A. (1999) CAP3: a DNA sequence assembly program. Genome Res., 9, 868-877.
6. Pertea,G., Huang,X., Liang,F., Antonescu,V., Sultana,R., Karamycheva,S., Lee,Y., White,J., Cheung,F., Parvizi,B., Tsai,J. and Quackenbush,J. (2002) TIGR Gene Indices Clustering Tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19, 651-652.
7. Iseli,C., Jongeneel,C.V. and Bucher,P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 138-148.
8. Wang,X. and Seed,B. (2003) Selection of oligonucleotide probes for protein coding sequences. Bioinformatics, 19, 796-802.
9. Lee,Y., Sultana,R., Pertea,G., Cho,J., Karamycheva,S., Tsai,J., Parvizi,B., Cheung,F., Antonescu,V., White,J., Holt,I., Liang,F. and Quackenbush,J. (2002) Cross-referencing eukaryotic genomes: TIGR Othologous Gene Alignments (TOGA). Genome Res., 12, 493-502.
10. Tsai,J., Sultana,R., Lee,Y., Pertea,G., Karamycheva,S., Anonescu,V., Cho,J., Parvizi,B., Cheung,F. and Quackenbush,J. (2001) RESOURCERER: a database for annotating and linking microarray resources with and cross species. Genome Biol., 2, software0002.1-software0002.4.
11. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The distributed annotation system. BMC Bioinformatics, 2 7.