The profile class: using sequence profiles
Keywords: manual

Next: profile() create Up: MODELLER command reference Previous: atom.residue residue Contents Index

#
The `profile` class: using sequence profiles

The `profile` class holds a sequence profile. Sequence profiles are similar to multiple alignments, and can contain gaps, but do not contain all of the information of the `alignment` class. Profiles can be matched against each other with profile.scan() or enriched from a sequence database with profile.build().

Subsections

- profile() -- create a new profile
- profile.read() -- read a profile of a sequence
- profile.write() -- write a profile
- profile.to_alignment() -- profile to alignment
- profile.scan() -- Compare a target profile against a database of profiles
- profile.build() -- Build a profile for a given sequence or alignment
- pssmdb() -- create a new PSSM database
- pssmdb.read() -- read a PSSM database from a file