Next: alignment() create Up: MODELLER command reference Previous: gbsa.Scorer() create Contents Index

The `alignment` class: comparison of sequences and structures

This section describes the commands for reading, writing, making, analyzing and using the alignments of sequences and structures (pairwise and multiple). For the underlying dynamic programming methods see Section A.1.

Subsections

alignment() -- create a new alignment
alignment.comments -- alignment file comments
alignment.append() -- read sequences and/or their alignment
alignment.clear() -- delete all sequences from the alignment
alignment.read_one() -- read sequences one by one from a file
alignment.check_structure_structure() -- check template structure superpositions
alignment.check_sequence_structure() -- check sequence/structure alignment for sanity
alignment.check() -- check alignment for modeling
alignment.compare_with() -- compare two alignments
alignment.append_model() -- copy model sequence and coordinates to alignment
alignment.append_sequence() -- add a sequence from one-letter codes
alignment.append_profile() -- add profile sequences to the alignment
alignment.write() -- write sequences and/or their alignment
alignment.edit() -- edit overhangs in alignment
alignment.describe() -- describe proteins
alignment.id_table() -- calculate percentage sequence identities
alignment.compare_sequences() -- compare sequences in alignment
alignment.align() -- align two (blocks of) sequences
alignment.align2d() -- align sequences with structures
alignment.malign() -- align two or more sequences
alignment.consensus() -- consensus sequence alignment
alignment.compare_structures() -- compare 3D structures given alignment
alignment.align3d() -- align two structures
alignment.malign3d() -- align two or more structures
alignment.salign() -- align two or more sequences/structures of proteins
- Features of proteins used for alignment
- Alignment of protein sequences
- Alignment of protein structures with sequences
- Alignment of protein structures
- Sub-optimal alignments
- Alignments using external restraints
- Gap penalties and correcting for gaps
- Useful SALIGN information and commands
alignment.to_profile() -- convert alignment to profile format
alignment.segment_matching() -- align segments

Ben Webb 2008-05-05

The alignment class: comparison of sequences and structures

The `alignment` class: comparison of sequences and structures