HMMGAP is a tool that is used within several other programs and can also be used as a standalone feature. HMMGAP takes two parameters: “Input Sequence” and “Gap Segment.” Gap Segment refers a segment of the input sequence containing gaps delimited with periods. HMMGAP returns the segment with highlighted putative TMS regions that are numbered relative to the entire sequence. The input segment does not have to contain gaps, but is usually determined by a Needleman Wunsch comparison.

HMMGAP can be accessed online here

To access the standalone version, type the following syntax in the terminal window

hmmgap.py <FULLSEQUENCE> <SEGMENT.WITH.GAPS> <OUT_FILE(optional)>