DNannotator: Annotation software tool kit for regional genomic sequences

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3729-3735

  Liu, Chunyu ^a,b,e   Bonner, Tom I ^c   Nguyen, Tu ^a   Lyons, Jennifer L ^d   Christian, Susan L ^a   Gershon, Elliot S ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b CENTRAL SOUTH UNIVERSITY   (China)

^c NATIONAL INSTITUTE OF MENTAL HEALTH   (United States)

^d UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^e BSLC ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; PRIMER DNA;

ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; CONTROLLED STUDY; EXPERIMENTAL DESIGN; GENBANK; GENE SEQUENCE; GENE TARGETING; GENETIC MARKER; INFORMATION PROCESSING; INTERNET; MARKER GENE; NOMENCLATURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOME 13; COMPUTER INTERFACE; DNA SEQUENCE; EVALUATION; GENOME; GENOMICS; HUMAN; METHODOLOGY; SEQUENCE TAGGED SITE;

CHROMOSOMES, HUMAN, PAIR 13; DNA PRIMERS; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEQUENCE TAGGED SITES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0043123004     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg542     Document Type: Article

References (23)

1. Ouzounis,C.A. and Karp,P.D. (2002) The past, present and future of genome-wide re-annotation. Genome Biol., 3, COMMENT 2001.
2. Camus,J.C., Pryor,M.J., Medigue,C. and Cole,S.T. (2002) Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology, 148, 2967-2973.
3. Carter,K., Oka,A., Tamiya,G. and Bellgard,M.I. (2001) Bioinformatics issues for automating the annotation of genomic sequences. Genome Inform. Ser. Workshop Genome Inform., 12, 204-211.
4. Harris,N.L. (1997) Genotator: a workbench for sequence annotation. Genome Res., 7, 754-762.
5. Makalowska,I., Ryan,J.F. and Baxevanis,A.D. (2001) GeneMachine: gene prediction and sequence annotation. Bioinformatics, 17, 843-844.
6. Bailey,L.C., Jr., Fischer,S., Schug,J., Crabtree,J., Gibson,M. and Overton,G.C. (1998) GAIA: framework annotation of genomic sequence. Genome Res., 8, 234-250.
7. Jareborg,N. and Durbin,R. (2000) Alfresco - a workbench for comparative genomic sequence analysis. Genome Res., 10, 1148-1157.
8. Glusman,G. and Lancet,D. (2000) GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses. Bioinformatics, 16, 482-483.
9. Taudien,S., Rump,A., Platzer,M., Drescher,B., Schattevoy,R., Gloeckner,G., Dette,M., Baumgart,C., Weber,J., Menzel,U. et al. (2000) RUMMAGE - a high-throughput sequence annotation system. Trends Genet., 16, 519-520.
10. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
11. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
12. Mott,R. (1997) ESTNOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
13. Wheelan,S.J., Church,D.M. and Ostell,J.M. (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res., 11, 1952-1957.
14. Schuler,G.D. (1998) Electronic PCR: bridging the gap between genome mapping and genome sequencing. Trends Biotechnol., 16, 456-459.
15. Rutherford,K., Parkhill,J., Crook,J., Horsnell,T., Rice,P., Rajandream,M.A. and Barrell,B. (2000) Artemis: sequence visualization and annotation. Bioinformatics, 16, 944-945.
16. Benson,D.A., Boguski,M.S., Lipman,D.J. and Ostell,J. (1997) GenBank. Nucleic Acids Res., 25, 1-6.
17. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The Distributed Annotation System. BMC Bioinformatics, 2, 7.
18. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
19. Detera-Wadleigh,S.D., Badner,J.A., Berrettini,W.H., Yoshikawa,T., Goldin,L.R., Turner,G., Rollins,D.Y., Moses,T., Sanders,A.R., Karkera,J.D. et al. (1999) A high-density genome scan detects evidence for a bipolar-disorder susceptibility locus on 13q32 and other potential loci on 1q32 and 18p11.2. Proc. Natl Acad. Sci. USA, 96, 5604-5609.
20. Liu,C., Badner,J.A., Christian,S.L., Guroff,J.J., Detera-Wadleigh,S.D. and Gershon,E.S. (2001) Fine mapping supports previous linkage evidence for a bipolar disorder susceptibility locus on 13q32. Am. J. Med. Genet., 105, 375-380.
21. Badner,J.A. and Gershon,E.S. (2002) Regional meta-analysis of published data supports linkage of autism with markers on chromosome 7. Mol. Psychiatry, 7, 56-66.
22. Blouin,J.L., Dombroski,B.A., Nath,S.K., Lasseter,V.K., Wolyniec,P.S., Nestadt,G., Thornquist,M., Ullrich,G., McGrath,J., Kasch,L. et al. (1998) Schizophrenia susceptibility loci on chromosomes 13q32 and 8p21. Nature Genet., 20, 70-73.
23. Brzustowicz,L.M., Honer,W.G., Chow,E.W., Little,D., Hogan,J., Hodgkinson,K. and Bassett,A.S. (1999) Linkage of familial schizophrenia to chromosome 13q32. Am. J. Hum. Genet., 65, 1096-1103.