ProDA

ProDA aligns homologous regions within unaligned protein sequences to detect and align complex domain architectures, including repeated, shuffled, and missing domains.

Key Features:

• Detection of homologous regions: Automates identification of homologous regions present in one or more sequences regardless of domain order.
• Local multiple alignments: Generates a collection of local multiple alignments for identified homologous regions.
• Handling of complex domain architectures: Accommodates repeated, shuffled, and missing domains in protein sequences.
• Conserved domain boundary detection: Accurately discerns conserved domain boundaries.
• Domain segment clustering: Effectively clusters domain segments based on detected homology.
• Benchmark evaluation: Evaluated on a subset of the BAliBASE benchmarking suite and demonstrated superior accuracy in boundary detection and domain-segment clustering compared to existing methods.

Scientific Applications:

• Protein structure and evolution: Facilitates analysis of evolutionary relationships and structural functions for proteins with complex domain arrangements.
• Homology assessment in non-standard proteins: Enables detection of homology among proteins with repeats, rearrangements, or nonstandard domain architectures.
• Alignment generation for downstream analyses: Produces local multiple alignments that support downstream structural and evolutionary analyses.

Methodology:

Automates detection of homologous regions, generates local multiple alignments for those regions, discerns conserved domain boundaries, and clusters domain segments.