PicXAA-Web

PicXAA-Web performs probabilistic non-progressive multiple sequence alignment of protein, DNA, and RNA sequences to maximize expected alignment accuracy while capturing local and global sequence similarity and accommodating RNA structural characteristics.

Key Features:

• Probabilistic Non-Progressive Alignment Algorithms: Implements the PicXAA and PicXAA-R probabilistic non-progressive algorithms that construct alignments from regions with high local similarity and aim to maximize expected accuracy.
• Multiple Sequence Alignment: Aligns multiple protein and DNA sequences by building alignments from regions of high local similarity to produce global alignments that reflect input sequence relationships.
• Structural RNA Alignment: Extends alignment capabilities to RNA sequences using the probabilistic framework of PicXAA-R to accommodate RNA structural characteristics for precise alignments.

Scientific Applications:

• Comparative Genomics: Analyzing evolutionary relationships by comparing genetic material across species.
• Protein Structure Prediction: Aligning homologous proteins to infer function.
• RNA Research: Investigating RNA structure–function relationships and interactions.
• Functional Annotation: Annotating genes and predicting functions based on sequence similarities.

Methodology:

Constructs alignments from regions with high local similarity; captures global and local sequence similarities to maximize expected accuracy; builds alignments progressively from high local similarity regions; uses a probabilistic framework in PicXAA-R to accommodate RNA structural characteristics.