AutoSNPdb

AutoSNPdb identifies single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) from DNA sequence data to support genetic variation analysis.

Key Features:

• Sequence identification and clustering: Uses BLAST to identify related sequences and CAP3 to cluster and align those sequences.
• SNP and indel detection: Employs autoSNP to parse CAP3 alignments and detect SNPs and indels.
• Error differentiation through redundancy: Evaluates redundancy at polymorphic sites to distinguish true SNPs from sequencing errors.
• Confidence measures for candidate SNPs: Computes redundancy and co-segregation of candidate SNPs within alignments as confidence metrics.
• Flexibility in input data: Accepts lists of related sequences or pre-assembled sequences for analysis.

Scientific Applications:

• Population genetics: Supports SNP and indel discovery for studies of genetic variation within and between populations.
• Evolutionary biology: Enables identification of polymorphisms for evolutionary and phylogenetic investigations.
• Personalized medicine: Provides SNP discovery relevant to disease susceptibility and personalized medicine research.

Methodology:

Integrates BLAST for sequence identification, CAP3 for clustering and alignment, and autoSNP for SNP and indel detection, and computes redundancy and co-segregation confidence measures.