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

• Ensembl
• GFF Files
• Transfac
• Jaspar
• GSC internal coexpression database
• Output files from several motif discovery programs
• NHGRI Encode: Encyclopedia of DNA elements project
• Crosslink information to
• Wormbase
• 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"?

Alignments

• 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

Motif discovery

• 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

Primer prediction