Sequence Analysis Tools生物信息学教学精品.ppt

The MEME/MAST Motif Discovery and Search tools MEME:Discover motifs (highly conserved regions) in groups of related DNA or protein sequences. MAST:Search sequence databases using motifs. /meme/website/intro.html Software Tools for Sequence Analysis General Packages: Open source Commercial UNIX only UNIX only WWW and X GUIs Comprehensive Widely available Similar structure to the GCG package Several GUIs (java, WWW, X) Excellent GUI including interactive graphical output Comprehensive Not comprehensive but allows access to EMBOSS Open source Windows, MacOS X, UNIX GCG Wisconsin Package Molecular biologists worldwide use the GCG? Wisconsin Package? as their software of choice for comprehensive sequence analysis. The Wisconsin Package meets research Genetics Computer Group Founded in 1982 as a service of the Department of Genetics at the University of Wisconsin, GCG became a private company in 1990 and was acquired by Oxford Molecular Group in 1997. The company was one of the pioneers of bioinformatics and its Wisconsin Package sequence analysis tools are widely used and well regarded throughout the pharmaceutical and biotechnology industries and in academia. EMBOSS EMBOSS (European Molecular Biology Open Software Suite) is an open source package of sequence analysis tools. This software covers a wide range of functionality and can handle data in a variety of formats Download address: /pub/EMBOSS/EMBOSS-2.8.0.tar.gz Only linux/unix version no version for win/dos Totally 150 programs Sequence alignment. Rapid database searching with sequence patterns. Protein motif identification, including domain analysis. Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats. Codon usage analysis for small genomes. Rapid identification of sequence patterns in large scale sequence sets. Presentation tools for publication. Bioinformatics Is the general topic of this talk, though I intend to concentrate on Bioinformatics as experienced by users