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几款常用的比较基因组学分析工具:Tools for Comparative Genomics  

2011-11-06 20:48:26|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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    VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.
http://genome.lbl.gov/vista/index.shtml

   Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

http://www.sanger.ac.uk/resources/software/artemis/

   M-GCAT is a tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased.

http://alggen.lsi.upc.es/recerca/align/mgcat/

    Metalife Genome Comparison Tool is a product that aims to provide the functionality to query, explore, analyze and visualize biological data in the context of completely and incompletely sequenced genomes. The functionality of the product is structured in several modules due to the complexity of the information.
    Metalife Genome Comparison Tool integrates algorithms for pairwise local alignments like BLAST, MegaBLAST and BLASTZ. Other algorithms such as cognitor and cogfinder are also integrated in the metalife genome comparison tool.

http://www.metalife.com/products/metalife_trinity/genome_comparison_tool.html



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