Bacterial Genomics: Software and experiments in silico

Software and experiments “in silico”

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

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

Microbial genomes comparative analysis

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.

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

An online service to design primers according to your needs.

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

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).