Biological Sequence Annotation Viewer — BioSAVE
BioSAVE (the E probably comes from "Viewer" somewhere) is a program for visualising DNA or protein sequences and annotations thereof. Annotations is used in a very broad sense here, encompassing any annotation that may be expressed in GFF format.
BioSAVE was initially created by Richard Pollock and Boris Adryan to visualise predicted transcription factor binding sites at various statistical cutoffs. The program then grew to support additional "tracks" of data, such as sequence conservation or ChIP enrichment data alongside the predicted motifs.
Since all of these data were read in from GFF and FASTA files, it was only a small step to extend the program to viewing protein sequences and a whole variety of possible annotations, including phosphorylation sites, protein structural annotations, DNA methylation sites and anything else that can be expressed in the versatile GFF format.
NEW (20/03/2008): A manuscript describing BioSAVE is accepted in BMC Bioinformatics. Please cite BMC Bioinformatics 2008, 9:157, if you find the software useful in your work.