Comparative Gene Finding

作者: Marina Axelson-Fisk

DOI:

关键词:

摘要: Comparative gene finding is a fairly new and emerging field within computational biology. The generation of finders has considerable number advantages over its single species predecessors, including higher prediction accuracy, the ability to annotate more varying features that previously have eluded approaches. In Chap. 2 we described some most common algorithms used as main in finding. this chapter exemplify corresponding comparative finding, ranging from similarity based techniques, pair hidden Markov models generalized models, mapping. Last present first attempts extend pairwise approaches multiple sequence Each section finished off by an example software using method question.

参考文章(35)
Haussler D, Reese Mg, Kulp D, Eeckman Fh, Integrating database homology in a probabilistic gene structure model pacific symposium on biocomputing. pp. 232- ,(1997)
David Haussler, Martin G. Reese, David Kulp, Frank H. Eeckman, A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA intelligent systems in molecular biology. ,vol. 4, pp. 134- 142 ,(1996)
Christopher B. Burge, Chapter 8 – Modeling dependencies in pre-mRNA splicing signals New Comprehensive Biochemistry. ,vol. 32, pp. 129- 164 ,(1998) , 10.1016/S0167-7306(08)60465-2
Sourav Chatterji, Lior Pachter, Reference based annotation with GeneMapper Genome Biology. ,vol. 7, pp. 1- 10 ,(2006) , 10.1186/GB-2006-7-4-R29
Ross C. Hardison, John Oeltjen, Webb Miller, Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome Genome Research. ,vol. 7, pp. 959- 966 ,(1997) , 10.1101/GR.7.10.959
Scott Schwartz, Zheng Zhang, Kelly A Frazer, Arian Smit, Cathy Riemer, John Bouck, Richard Gibbs, Ross Hardison, Webb Miller, PipMaker—A Web Server for Aligning Two Genomic DNA Sequences Genome Research. ,vol. 10, pp. 577- 586 ,(2000) , 10.1101/GR.10.4.577
Colin Dewey, Jia Qian Wu, Simon Cawley, Marina Alexandersson, Richard Gibbs, Lior Pachter, None, Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse and Rat Genome Research. ,vol. 14, pp. 661- 664 ,(2004) , 10.1101/GR.1939804
Warren Gish, David J. States, Identification of protein coding regions by database similarity search. Nature Genetics. ,vol. 3, pp. 266- 272 ,(1993) , 10.1038/NG0393-266
Eric E. Snyder, Gary D. Stormo, Identification of protein coding regions in genomic DNA. Journal of Molecular Biology. ,vol. 248, pp. 1- 18 ,(1995) , 10.1006/JMBI.1995.0198
Lior Pachter, Marina Alexandersson, Simon Cawley, Applications of generalized pair hidden Markov models to alignment and gene finding problems. Journal of Computational Biology. ,vol. 9, pp. 389- 399 ,(2002) , 10.1089/10665270252935520