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The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you ...

If you're looking for an exact match, you don't really need a complex aligner. Perl regular expressions are pretty powerful at string transformations or conditional matching of substrings. For example, to find all matches of AASYWSRA in a nucleotide sequence $seq, you can do: @matches = $seq =~ m/AA[CG][CT][AT][CG][AG]A/g; The [] brackets are known as ...

Bacterial DNA evolution is like other evolution in the sense that the mutation rates are probably random and biased somewhat by the physical and chemical structure of DNA as well as the presence and activity of DNA repair enzymes. The mutation protocols for preparing mutant libraries from UV or chemical mutagens are a good place to start I would think - ...