BioSAVE

MRC Laboratory of Molecular Biology, 2007

BioSAVE (Biological Sequence and Annotation Viewer) is a piece of Mac OS X software for viewing annotations of DNA and protein sequences. The program was written in Objective C using Apple's Cocoa frameworks.

BioSAVE natively reads sequence annotations in GFF format, but also supports script plug-ins to convert other annotation formats to GFF on-the-fly from the comfort of the open dialog box. Sequence data can be read in either plain text (for single sequences) or FASTA format.

If the annotation file contains statistical scorings, BioSAVE will present two sliders allowing upper and lower statistical cutoffs to be set; BioSAVE will dynamically show only those motifs which fall within the specified range. Even better, the motifs that do fall within the range are shaded dynamically to represent approximately where in the range they fall (darker shading can be set to represent either higher or lower scores).

BioSAVE can also display an arbitrary number of additional annotation tracks along the length of the sequence (see screenshot, right). This allows additional data, such as ChIP enrichment or evolutionary conservation, to be quickly viewed in place. Since the tracks utilise the very same plug-in architecture as the main annotation, a script could easily be used to pull the track data live from the web, a MySQL database or the local file system.

BioSAVE can found, along with considerable supporting documentation and example data sets, on the Theoretical and Computational Biology group page at the MRC-LMB. It requires Mac OS X 10.3.9 and up.