VariVis: a visualisation tool for variation databases
The VariVis system is a collection of Perl scripts designed to provide a basic set of sequence and variation visualisation tools specifically for LSDBs. It is designed to work in parallel with a database's existing user interface and storage and retrieval back-end. For this reason, VariVis has been designed so that it can gather data from a wide variety of sources including Database Management Systems (DBMSs) such as MySQL, Oracle, PostgreSQL through to flat-file repositories such as Comma or Tab delimited text files. Gene sequences and annotations can be provided to the software either locally, using a large number of sequence file formats, such as FASTA, BSML and Tinyseq; or VariVis can be directed to automatically retrieve such data from any of several online sequence databases such as GenBank or EMBL.
VariVis is capable of producing two different conceptual views based on the sequence and variation data provided. The first displays the gene sequence and overlays positions where variation is present. Clicking the variant symbols provides the user with a brief overview of the data extracted from the database, from which the user can link to the variant entry in the database, or perform simple PubMed and Google Scholar searches to find published articles on the variant.
The second view, the "Gel View," has the same functionality as the first viewing option, but this time orientates the sequence vertically, allowing for an unbroken stream of data. Theoretically, it is possible that any given nucleotide in a gene can be mutated to any other nucleotide base, deleted entirely, or have an adjacent insertion. The "Gel View" displays all possible nucleotide combinations for each position, highlighting the nucleotides present in the reference sequence and any variations in contrasting colours.
In both views, the software also displays any structural annotations, such as promoter sequences, poly-A sites, and UTRs that are present in the sequence file being used. The software also provides access to the raw sequence data, allowing users to copy or download the entire sequence, or specific chunks, negating the need to navigate to a dedicated sequence database.
VariVis can be run on any web server capable of executing Perl 5.6.1 CGI scripts. The system makes use of the external BioPerl, DBI and CGI modules, and these must be installed prior to use. Installation of both modules can be performed using either the CPAN or ActiveState Package Managers.
For more information: Timothy D. Smith