PACAS

PACAS performs pairwise comparisons of aligned subsequences within protein sequence alignments to quantify conservation of user-defined sub-regions and contrast their conservation with the remainder of the alignment.

Key Features:

• Sub-region Specific Analysis: Enables definition and analysis of user-specified sub-regions within protein alignments to examine conservation across different parts of the sequence.
• Comparative Conservation Measures: Computes measures of conservation between pairs of sequences and contrasts them with the rest of the alignment to identify regions under distinct evolutionary pressures.
• Integration with Low Complexity Region Analysis: Analyzes low complexity regions (LCRs), including examples in Plasmodium genes AMA1 and CSP, and accepts LCR annotations produced by SEG or provided manually.

Scientific Applications:

• Evolutionary Biology: Assess conservation across sub-regions to infer evolutionary pressures and functional constraints on specific protein domains.
• Genomic Studies: Analyze LCRs to investigate genomic stability and variability in organisms with complex genomes such as Plasmodium.

Methodology:

Requires a FASTA file containing accession numbers and aligned protein sequences (sequences aligned on a single line and of equal length); requires an output file with the same name as the FASTA to indicate low complexity regions (can be generated by SEG or provided manually); comprises the files Pacas.py, Pacas_FB.pl, and Pacas_CP.pl which must reside in the same directory as the data files for execution.