Homology search for genes

Bioinformatics

Volumn 23, Issue 13, 2007, Pages

  Cui, Xuefeng ^a   Vinař, Tomáš ^b   Brejová, Brońa ^b   Shasha, Dennis ^c   Li, Ming ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^c POLYTECHNIC UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AUTOMATION; CONFERENCE PAPER; CORRELATION ANALYSIS; EVOLUTIONARY HOMOLOGY; EXON; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENOME ANALYSIS; HIDDEN MARKOV MODEL; MOUSE; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; RELIABILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPLICEOSOME;

EID: 34547852257     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm225     Document Type: Conference Paper

References (22)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Benson,G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
3. Birney,E. et al. (2004) GeneWise and GenomeWise. Genome Res. 14, 988-995.
4. Brejová.B et al. (2005) ExonHunter: A comprehensive approach to gene finding. Bioinformatics, 21, i57-i65. Intelligent Systems for Molecular Biology (ISMB 2005).
5. Burge, C. (1997) Identification of Genes in Human Genomic DNA. PhD thesis, Stanford University.
6. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
7. Chatterji, S. and Pachter, L. (2004) Multiple organism gene finding by collapsed Gibbs sampling. In Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), ACM Press, New York, NY, USA pp. 187-193.
8. Florea,L. et al. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
9. Gerhard,D.S. et al. (2004) The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Res., 14, 2121-2127.
10. Guigo,R. et al. (2006) EGASP: The human ENCODE Genome Annotation Assessment Project. Genome Biol., 7, 1-31.
11. Keibler,E. and Brent,M.R. (2003) Eval: A software package for analysis of genome annotations. BMC Bioinformatics, 4, 50.
12. Kent,W.J. (2002) BLAT: The BLAST-like alignment tool. Genome Res., 12, 656-664.
13. Kisman,D. et al. (2005) tPatternHunter: Gapped, fast and sensitive translated homology search. Bioinformatics, 21, 542-544.
14. Kuhn,R.M. et al. (2007) The UCSC genome browser database: Update 2007. Nucleic Acids Res., 35, 668-573. http://genome.ucse.edu/
15. Ma,B. et al. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
16. Meyer, I.M. and Durbin,R. (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res., 32, 776-783.
17. Rabiner,L.R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc. of the IEEE, 77, 257-286.
18. Smit,A. et al. (2006) RepeatMasker http://www.repeatmasker.org/
19. Stanke,M. and Waack,S. (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics, 19, 215-225. European Conference on Computational Biology (ECCB 2003).
20. Volfovsky, N. et al. (2003) Computational discovery of internal micro-exons. Genome Res., 13, 1216-1221.
21. Wheeler,D.L. et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 34 173-180. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
22. Wu,T.D. and Watanabe,C.K. (2005) GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875.