-zmax allowed distance between genes. This should be roughly the upper limit of intergenic distances in the genome, meaning 99% of genes are closer than-z(seehere for an example). -Rrandomize gene order of the query, to estimate false discovery rate ...
we have not restricted the items expressible in GFF to a specified set of feature types (splice sites, exons etc.) with defined semantics. Therefore, in order for the information in a gff file to be useful to somebody else, the person producing the features must describe the meaning of th...
Treaty text is language that requires meaning in order to apply it to the concrete facts presented to the adjudicator. The process to come to this meaning is interpretation. This is not particular to treaty texts. Interpretation normally presupposes an authoritative text, something authored, whether...
for each duplicate, as up to 5 intervening genes are allowed (by the option-s). A hypothetical example is shown in the figure below. In such a case, hypothetical genes 1-3 would be matched twice (once normally, once with the intervening gene 1b), meaning the block will be counted ...