Greetings,
Often, wet lab biologists will come to me with DNA/cDNA sequences and no idea of which tools (besides BLAST) they can use to analyse them. I've found that for them, and oftentimes for me too, the limiting factors in analysis become (1) the number of specialized tools of whose existence we are aware and (2) the time needed to submit our sequence through all of these tools. The parsing of the results themselves are often trivial: homologies are either present or absent, SNPs are there or aren't, etc.
Also, the first steps of the decision tree for choosing which analysis to perform are often relatively simple, too. Nucleotide sequence: is it DNA or RNA? If it is DNA: Where does it map? Are there SNPs, Indels? If it is RNA:, is it a known splice variant or a novel one? If it does not map anywhere, does it have an ORF? Etc.
Thus, I have been wondering: is anyone aware of efforts having been put forth toward creating an heuristic driven, fully integrated, one-stop "automagical" pipeline to identify/analyze sequences of interest? If not, would such software be feasible, and do you believe wet lab biologists or bioinformaticians would use it?
