FASTA API (EBI)

FASTA API (EBI) performs sequence similarity searches and statistical evaluation of protein and DNA sequences, including translation of DNA for protein queries and detection of local and periodic similarities.

Key Features:

• FASTA Program: Refined from FASTP, it searches protein and DNA databases, translates DNA for protein queries, and links multiple regions via pairwise similarity scoring to increase sensitivity and accuracy.
• RDF2 Program: Evaluates the statistical significance of similarity scores using a shuffling method that preserves local sequence composition.
• LFASTA Program: Identifies and displays regions of local similarity exceeding a threshold using the same scoring parameters and alignment algorithms as FASTA and producing "graphic matrix" plots or individual alignments.
• Scoring Matrices: Employs a variety of scoring matrices to compare DNA or protein sequences, enabling parameter choices appropriate to different sequence types.

Scientific Applications:

• Sequence Database Searches: Searches across protein and DNA databases to identify homologous sequences.
• Similarity Score Evaluation: Determines the statistical significance of sequence similarities to support functional annotation and evolutionary studies.
• Identification of Periodic Structures: Detects periodic patterns based on local sequence similarity to analyze structural motifs in proteins and nucleic acids.

Methodology:

Uses multiple scoring matrices to compare DNA and protein sequences; translates DNA sequences for protein queries; computes pairwise similarity scores that can link multiple regions; applies shuffling that preserves local sequence composition to assess significance; and employs threshold-based local similarity detection with alignment algorithms and "graphic matrix" plots or individual alignments.