Bio.Compass package

Module contents

Code to deal with COMPASS output, a program for profile/profile comparison.

Compass is described in:

Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol. 2003 Feb 7;326(1):317-36.

Tested with COMPASS 1.24.

Read a COMPASS file containing one COMPASS record.


Iterate over records in a COMPASS file.

class Bio.Compass.Record

Bases: object

Hold information from one compass hit.

Ali1 is the query, Ali2 the hit.


Initialize the class.


Return the length of the query covered in the alignment.


Return the length of the hit covered in the alignment.