2012年9月27日星期四

GBrowse and biotoolbox - sets of perl programs

1. http://gmod.org/wiki/GBrowse


GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Use a variety of premade glyphs or create your own.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.
  • Connectivity to different databases, including BioSQL and Chado.
  • Multi-language support.
  • Third-party feature loading.
  • Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)

2. http://code.google.com/p/biotoolbox/

Lists of programs organized by function.

Data collection

Data analysis

Dataset manipulation

File format conversion

Finding features

Genome annotation

Illumina sequencing, BAM files

Nucleosome Analysis

Microarray

SNP calling

Miscellaneous

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