Guidance

Bioinformatics: online tools

A series of tools developed by Public Health England's (PHE's) bioinformatics unit as part of larger genomics-based projects.

One of the functions of PHE’s bioinformatics unit is to develop tools as part of larger genomics-based projects. The tools with wider generic uses are available here for use across the scientific community.

Genome annotation browser

The genome annotation browser searches all complete microbial genomes for features that are described with a particular keyword. The output from the program display all relevant information for those features matching the query including their sequence.

AFLP fragment predictor program (ALFIE)

ALFIE predicts fragment sizes resulting from restriction endonuclease digestion and subsequent amplification in an AFLP reaction. All currently sequenced genomes are available for querying. A list of target sequences may also be supplied.

Gene extractor

Gene extractor will extract all the coding sequences from a genbank file that contains multiple genes. The output will be displayed as FASTA format.

Motifs or primers: unique to pooled sets (MOP-UPs)

MOP-UPs will search alignments for primers or amino acid motifs that are specific to user-defined groups of sequences within the alignment.

Virulence searcher

Virulence searcher predicts potential virulence factors in unannotated genomes by predicting genes and searching the putative proteins for virulence-related amino acid motifs.

EMBOSS

EMBOSS is a suite of molecular biology tools which perform functions including:

  • alignments
  • DNA or protein editing
  • repeat finding
  • composition analysis

Double artemis comparison tool (ACT)

Double ACT can easily generate the comparison file necessary to run the genome comparison tool ACT provided by the Sanger Centre.

Please email us with suggested improvements to these tools and ideas for new tools that would be applicable to generic methodologies.

Published 1 April 2013