Health protection – 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

VNTR diversity and confidence extractor (V-DICE)

V-DICE will calculate the diversity index of VNTR loci, plus confidence intervals. This tool provides statistical evidence of repeat variability for known loci, which may aid assay development.

Synonymous bases in nucleotide sequences (SynBin)

SynBin identifies synonymous and non-synonymous mutations in DNA sequences. This tool allows multiple query sequences to be compared to one of a list of user-submitted reference sequences. It will provide a graphical report of mutation location and status.

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.

Assembly tool

Assembly tool takes traces belonging to a single locus from one strain or isolate and assembles them. The resulting consensus sequence will be scored for quality. If a reference sequence or sequences are supplied then the consensus sequence will be aligned to each one and the closest match reported along with the corresponding alignment.

Variable region finder

Variable region finder is a tool that finds regions of difference between strains where there are at least 3 genome sequences available. This application will allow scientists to quickly determine regions that will be of interest when studying phenotypic difference or designing typing assays.

PFGE predictor

PFGE predictor takes sequenced genome and predicts the fragment sizes that will be produced when cut with a particular restriction endonuclease. The sequence and genes that lie on each fragment can be determined.

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