Table 1 A sample of sources available on experimentally, computationally derived gene annotations and sequence pattern discovery programs
Annotation Type | Source | Reference |
|---|---|---|
Alternative splicing | AltSplice and AltExtron – Computationally derived splicing events. AEdb – splicing events manually generated from the literature. | [32] |
| Â | Swiss-Prot/TrEMBL http://au.expasy.org/sprot/ | [35-37] |
Polymorphic sequence variations | [38] | |
Predicting RNA secondary structures | [34] | |
Predicting protein motif/domains/structural similarities | [39] | |
Human gene mutations | [40] [41] | |
Predicting transcription factor binding sites | MAPPER http://bio.chip.org/mapper | [42] |
Predicting exonic splicing enhancer sites | ESEFinder http://rulai.cshl.edu/tools/ESE RESCUE-ESE http://genes.mit.edu/burgelab/rescue-ese/ | [43] [44] |
Predicting promoter elements | SIGNAL SCAN http://thr.cit.nih.gov/molbio/signal/ | [45] |
Post-translational modifications | Swiss-Prot/TrEMBL http://au.expasy.org/sprot/ | [35-37] |
Predicting post-translational modifications | NetAcet – N-terminal acetylation in eukaryotic proteins. NetNGlyc – N-linked glycosylation sites in human proteins. NetOGlyc – O-GalNAc (mucin type) glycosylation sites in mammalian proteins. NetPhos – Serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins. ProP – Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences. YinOYang – O-(beta)-GlcNAc glycosylation and Yin-Yang sites (intracellular/nuclear proteins). All above web server programs can be found at http://www.cbs.dtu.dk/services/ | [46] [47] [48] [49] |
Protein-protein interaction data | InterDom http://interdom.lit.org.sg/ BIND http://bind.ca/ | [50] [51] [52] [53] |