We have to manually assemble all this into one prediction. This can be done on the Netgene2 and DNA sequence outputs using biro and fluorescent marker. The following guidelines may help. Reported splice site quality is not a completely robust guide to usage. Context dependence is also important.
Splice sites tend to be overpredicted.
Once the prediction is completed, we can check it in the next exercise. Gene prediction by homology using GeneWise Usually nowadays, related sequences are already present in the databases. When available these may be the fastest way to get a good gene prediction. Often this prediction will be more reliable than the coding bias predictions though one should be aware of the possibility of sequence error, differential splicing etc. We've prepared files with the human DNA and a homologous chicken protein to compare.