An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

Journal of Genetics

Volumn 80, Issue 1, 2001, Pages 9-16

  Lynn, Andrew M ^a   Jain, Chakresh Kumar ^a   Kosalai, K ^a   Barman, Pranjan ^a   Thakur, Nupur ^a   Batra, Harish ^a   Bhattacharya, Alok ^a  

^a JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

BLAST; Computational genomics; DNA sequence; Fourier analysis; GeneScan; Genome annotation

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; EUKARYOTIC CELL; FOURIER ANALYSIS; GENETICS; GENOMICS; MICROBIAL GENETICS; MOLECULAR EVOLUTION; PLASMODIUM FALCIPARUM;

ALGORITHMS; ANIMALS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FOURIER ANALYSIS; GENETICS, MICROBIAL; GENOMICS; PLASMODIUM FALCIPARUM; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0035528185     PISSN: 00221333     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02811413     Document Type: Article

References (24)

1. Adams M. D., Celniker S. E., Holt R. A., Evans C. A., Gocayne J. D., Amanatides P. G. et al. 2000 The genome sequence of Drosophila melanogaster. Science 287, 2185-2195.
2. Alm R. A., Ling L. S., Moir D. T., King B. L., Brown E. D. Doig P. C. et al. 1999 Genomic sequence comparison of two unrelated isolates of human gastric pathogen Helicobacter pylori. Nature 397, 176-180.
3. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W. and Lipman D. J. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
4. Anderson S. G., Zomorodipour A., Andersson J. O., Sicheritz-Ponten T., Alsmark U. C., Podowski R. M. et al. 1998 The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396, 132-143.
5. The Arabidopsis Genome Initiative 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
6. Bhattacharya A., Bhattacharya S., Joshi A., Ramachandran S. and Ramaswamy R. 2000 Identification of parasitic genes by computational methods. Parasitol. Today 16, 127-131.
7. Bowman S., Lawson D., Basham D., Brown D., Chillingworth T., Churcher C. M. et al. 1999 The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532-538.
8. The C. elegans Sequencing Consortium 1998 Genome sequence of the nematode C. elegans: a platform for investigative biology. Science 282, 2012-2018.
9. Cole S. J., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D. et al. 1998 Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537-544.
10. Fickett J. W. 1982 Recognition of protein coding regions in genomic DNA. Nucl. Acids Res. 10, 5303-5318.
11. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R. et al. 1995 Whole genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
12. Fraser C. M., Casjens S., Huang W. M., Sutton S. G., Clayton R., Lathigra R. et al. 1997 Genomic sequence of a Lyme disease spirochaete, Borrelia borgdorferi. Nature 390, 580-586.
13. Haussler D. 1998 Computational gene finding. Trends Biochem. Sci. suppl. 'Trends in Bioinformatics' 12-15.
14. Heidelberg J F., Eisen J. A., Nelson W. C., Clayton R. A., Gwinn M. L., Dodson R. J. et al. 2000 DNA sequence of both the chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477-484.
15. Lee P. S. and Lee K. H. 2000 Genome analysis. Curr. Opin. Biotechnol. 11, 171-175.
16. Lewis S., Ashburner M. and Reese M. G. 2000 Annotating eukaryote genomes. Curr. Opin Struct. Biol. 10, 349-354.
17. Nierman W. C., Eisen J. A., Fleischmann R. D. and Fraser C. M. 2000 Genome data: what do we learn? Curr. Opin. Struct. Biol. 10, 343-248.
18. Parkhill J., Achtman M., James K. D., Bentley S. D., Churcher C., Klee S. R. et al. 2000 Complete DNA sequence of a serogroup A strain of Neisseria meningitidis. Nature 404, 502-506.
19. Ramakrishna R. and Srinivasan R. 1999 Gene identification in bacterial and organellar genomes using GeneScan. Comput. Chem. 23, 165-174.
20. Reese M. G., Hartzell G., Harris N. L., Ohler U., Abril J. F. and Lewis S. F. 2000 Genome annotation assessment in Drosophila melanogaster. Genome Res. 10, 483-501.
21. Short N., Dennis C. and Cohen B. (ed.) 1997 The yeast genome directory. Nature 387, suppl. 1-105.
22. Simpson A. J., Reinach F. C., Arruda P., Abren F. A., Acencio M., Alvarenga R. et al. 2000 The genomic sequence of a plant pathogen Xylella fastidiosa. Nature 406, 151-157.
23. Tiwari S., Ramachandran S., Bhattacharya A., Bhattacharya S. and Ramaswamy R. 1997 Prediction of probable genes by Fourier analysis of genome sequences. CABIOS 13, 263-270.
24. Wisconsin Package Version 10, Genetics Computer Group (GCG), Madison, USA.