- GRIT A tool for transcript discovery and quantification via the integrated analysis of CAGE, RAMPAGE, RNAseq, and poly(A)-seq data
- cis-analyst Search for clusters of transcription factor binding sites.
- Promoter Prediction - U. Ohler A statistical tool for the prediction of transcription start sites in D. melanogaster.
- Promoter Prediction - M.G. Reese A neural network based program to find possible transcription promoters.
- Splice Site Prediction A neural network based program to find possible 5' and 3' splice sites.
- Genie Gene finder based on Hidden Markov Models (HMM)
- Genotator Sequence annotation workbench by Nomi Harris (1996-97).
Other Analysis Tools
- Stubb - S. Sinha, E.D. Siggia Allows users to look for clusters of transcription factor binding sites in one or two aligned species and for fly data view the results superimposed on the D.melanogaster annotations via Gbrowse. A facility for viewing the site distribution within modules is included.
- Target Explorer - A. Sosinsky Allows users to create customized libraries of transcription factor binding site matrices, search for clusters and combinations of binding sites, retrieve FlyBase annotation for nearby genes, and generate graphical representations of binding sites.