SLAM web server for comparative gene finding and alignment

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3507-3509

  Cawley, Simon ^c   Pachter, Lior ^a   Alexandersson, Marina ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b FRAUNHOFER CHALMERS CENTRE   (Sweden)

^c Thermo Fisher Scientific   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; COMPARATIVE GENE MAPPING; COMPUTER PROGRAM; CONTROLLED STUDY; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; HUMAN; HUMAN GENOME; INTERNET; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; DNA SEQUENCE; GENOMICS; METHODOLOGY; MOUSE; NUCLEOTIDE SEQUENCE; PROBABILITY; RAT;

MESSENGER RNA; PEPTIDE; UNTRANSLATED RNA;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; GENE COMPONENTS; GENOMICS; HUMANS; INTERNET; MARKOV CHAINS; MICE; PEPTIDES; RATS; RNA, MESSENGER; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0042622343     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg583     Document Type: Article

References (13)

1. Alexandersson,M., Cawley,S. and Pachter,L. (2003) SLAM - cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res., 13, 496-502.
2. Batzoglou,S., Pachter,L., Mesirov,J.P., Berger,B. and Lander,E.S. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res., 10, 950-958.
3. Bafna,V. and Huson,D.H. (2000) The conserved exon method for gene finding. ISMB'00: Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (2000), 3-12.
4. Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 1, S1-S9.
5. Parra,G., Agarwal,P., Abril,J.F., Wiehe,T., Fickett,J.W. and Guigó,R, (2003) Comparative gene prediction in human and mouse. Genome Res., 13, 108-117.
6. Pachter,L., Alexandersson,M. and Cawley,S. (2002) Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comp. Biol., 9, 389-399.
7. Burge,C. and Karlin,T. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
8. Reese,M.G., Kulp,D., Tammana,H. and Haussler,D. (2000) Genie - Gene finding in Drosophila melanogaster. Genome Res., 10, 529-538.
9. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, UK.
10. Bray,N., Dubchak,I. and Pachter,L. (2003) AVID: a global alignment program. Genome Res., 13, 97-102.
11. Waterston,R.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
12. Karolchik,D., Baertsch,R., Diekhans,M., Frey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M., Schwartz,M., Sugnet,C.W., Thomas,D.J., et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51-54.
13. Mural,R., Adams,M.D., Myers,E.W., Smith,H.O., Miklos,G.L., Wides,R., Halpern,A., Li,P.W., Sutton,G.G., Nadeau,J. et al. (2002) A comparison of whole-genome-shotgun-derived mouse chromosome 16 and the human genome. Science, 296, 1667-1671.