What Can Sockeye Do
Full features 3D browser
- Versatile, state of the art 3D workspace, optimized for fast data access, visual and computational analysis.
Access multiple data sources
- GFF Files
- GSC internal coexpression database
- Output files from several motif discovery programs
- NHGRI Encode: Encyclopedia of DNA elements project
- Crosslink information to
- Geneview (EnsEMBL)
Work out Relationships between genomic features
- Functional relationsships, like homology, orthology, cooexpression etc
- Relationships based on genomic locations, thus allowing to answer questions like
- "show me all scan results that fall into coding regions"?
- "show me all discovered motifs that are located withing CPG islands"?
- "which of these binding sites fall within the 3000 base upstream region of the closest gene"?
- Extremely powerfull and generic alignment postprocessing including various smoothing methods and statistical analysis
- For complete list of alignment algorithms supported by Sockeye, please view Algorithms page
- Multiple flexible postprocessing methods based on feature sets allows for quick problem specific assesment of the relevance of the discovered featured
- For complete list of motif discovery algorithms supported by Sockeye, please view Algorithms page
Sequence scanning and analysis
- Scan with PWMs or sequence motifs
- using PWMs TRANSFAC or JASPAR
- using PWMs generated by various discovery programs
- using custom PWMs
- specifying a consensus string and number of mismatches
- work with masked or unmasked sequences
- Analyse the information content of a sequence or part of a sequence
Page last modified Feb 06, 2007