Help with GOtchaGOtcha requires very few parameters in order to run. You need a sequence (DNA or Protein), choose genomes against which to compare your sequence, select evidence codes for the annotations you are prepared to accept and select a cutoff. GOtcha does all the rest.
Sequence inputGOtcha can take a sequence in any format accepted by EMBOSS in three ways. Please select the appropriate method.
The real decision is whether to include IEA annotations or not.