This contribution presented a computational method to identify novel gastric cancer related genes based on known related ones by shortest path algorithm and PPI network.
Algorithms, based on known ligation patterns [14], [22], have been developed that identify false positives and reduce the loss of resolution when complex mixtures such as full-genome transcripts are analyzed on hexamer arrays [14].
Overall, we recommend using the mapping algorithm based on known exon annotation and Scripture combination at a low sequencing depth, and the TopHat and Scripture strategy with high sequencing coverage.
A high-probability CaM-binding site in BRI1 was predicted to occur in subdomain VIa of the kinase domain using an algorithm based on known binding proteins (http://calcium.uhnres.utoronto.ca/ctdb/ctdb/home.html), and a synthetic peptide corresponding to the predicted CaM-binding domain was found to interact with CaM in vitro.
Most of these algorithms are based on known binding peptides whose sequences have been used for the characterization of binding motifs or profiles.
There are a number of algorithms available based on known experience of what kinds of sequences are most likely to give an immune response, e.g., Expasy (http://www.expasy.org/tools/) IEDB website (http://tools.immuneepitope.org/tools/bcell/iedb_input), or Antigen Profiler (http://www.pierce-antibodies.com/custom-antibodies/peptide-design-antigen-profiler.cfm).
The algorithm was evaluated based on known gene disease and animal model disease associations using ROC curves and manually assessing a subset of the diseases with their highly ranked models and, consequently, gene candidates.
Based on known zebrafish pre-miRNAs, we designed a zebrafish-specific algorithm of ZmirP (zebrafish miRNA prediction), with 8 new and 57 previously reported sequence and structure features.
They may create their own algorithms to describe their learning, rather than require humans to program them based on known rules.
An algorithm was constructed to assess the self-consistency of the quantitation based on known relationships between the elutriated fractions.
