Bacterial Genomics: Software and experiments in silico


Software and experiments “in silico”

http://emboss.sourceforge.net/

EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.

http://insilico.ehu.es/

PCR, PCR-RFLP, AFLP-PCR, PFGE and endonuclease digestion data, etc

http://mbgd.genome.ad.jp/

Microbial genomes comparative analysis

http://img.jgi.doe.gov/v1.1/main.cgi

The Integrated Microbial Genomes (IMG) system provides a framework for comparative analysis of the genomes sequenced by the Joint Genome Institute. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.

http://www.cbs.dtu.dk/staff/thomas/pyphy/

A phylogenomic approach to microbial evolution. It generates a tree for each gene present in the list.

http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi

An online service to design primers according to your needs.

http://cobamide2.bio.pitt.edu/computer.htm

A list of freely available software developed by Prof. Jeff Lawrence.

http://www.tigr.org/software/transterm.html

TransTerm is a program developed by TIGR that finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that provides an estimate of its probability of being a true terminator. 

Virtual PCR

PCR against selected genomes. Data is obtained by performing blast at NCBI.

UCSC In-silico PCR

PCR against selected genomes. PCR is very stringent (no mismatches allowed).




Main