Locating Motifs in Context

Our job here is to locate possible NtcA binding sites in context: for each possible binding site, which open reading frames is it near? (There are more detailed specifications available.) The list of possible binding sites was produced by the FindMotif.pl program, which output to motif.hits.

Part of the job involves reading data in the 7120DB.DAT file, which is in a format more congenial to computers than to humans. (Take a peek.) That can get interesting, as the Reading A Binary File section of these notes attests.

The final program, find-context.pl, can be downloaded or viewed .