Alignment_engines

Engines performing alignments of sequences or structures Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and S. Marillet and R. Tetley

Main classes:

• T_Alignment_engine : Base engine for making alignments between structures and sequences.

• T_Aligner_sequence_seqan_wrapper : Wrapper of the Seqan algorithm for aligning pairwise sequences

• T_Alignment_engine_sequences_seqan : Engine for making alignments between sequences using Seqan.

• T_Alignment_engine_structures : Base engine for making alignments between structures.

• T_Aligner_structure_apurva_wrapper : Wrapper of the Apurva algorithm for aligning pairwise structures

• T_Alignment_engine_structures_apurva : Base engine for making alignments between structures using Apurva.

• T_Alignment_engine_structures_identity : Base engine for making alignments between two identical structures (in different conformations).

• T_Alignment_engine_structures_iterative_identity : Base engine for making queries in a identity alignment setting for a best local fit

• T_Alignment_engine_structures_kpax : Base engine for making alignments between structures using Kpax.

• T_Chains_residues_contiguous_indexer : Data structure to handle the contiguous indices of residues/un its in a chain even in the presence of missing residues/units.

• T_Alignment_sequences_module : Module which computes a pairwise alignment of two sequences

• T_Alignment_structures_module : Module which computes a pairwise alignment of two structures