Would anyone out there have a program capable of searching
GenBank (or EMBL) looking for perfect matches to short (6-8 nucleotide long)
sequences, but instead of searching the entire database, searching only
those parts of the (human) sequence files that would be present in mRNA, ie.
5' untranslated regions, exons, and 3' untranslated regions.
[Ideally, I would run one program that would answer the question, "Which
sequenced gene(s) has at least one exact match to each of the following set of
short sequences ?".] So far, I've not been able to locate a program capable of
deciphering the feature tables well enough to make the mRNA sequence.
Any ideas ??
With thanks in advance,
g_lennon at icrf.ac.uk