Jalview

Jalview performs interactive editing, analysis, and annotation of multiple sequence alignments to support comparative sequence and structural investigations.

Key Features:

• Multiple sequence alignment editing: Provides interactive editing and annotation of multiple sequence alignments.
• Alignment visualization: Offers multiple views and alignment overviews for inspection of conserved regions and sequence variation.
• Linked structure display (Jmol): Integrates linked structure display via Jmol to correlate sequence positions with molecular structures.
• Web-service sequence alignment: Performs sequence alignment by invoking external web services.
• Secondary structure prediction: Requests secondary structure prediction through web services.
• Data retrieval from public databases: Retrieves alignments, sequences, annotations, and structures from public databases via web services.
• DAS 1.53 support: Connects to DAS 1.53-compliant sequence and annotation servers for data integration.
• Analytical methods: Supports phylogenetic analyses and principal components analysis (PCA) on alignments.

Scientific Applications:

• Phylogenetic analysis: Reconstruction and visualization of phylogenetic relationships from multiple sequence alignments.
• Structural interpretation of variation: Mapping sequence variation onto molecular structures to assess structural implications.
• Principal components analysis (PCA): Summarizing major axes of variation in sequence datasets using PCA.
• Integrative annotation and retrieval: Combining retrieved alignments, sequences, annotations, and structures from public databases for comparative analyses.

Methodology:

Uses web services for sequence alignment and secondary structure prediction, integrates Jmol for linked structure display, and retrieves data from DAS 1.53-compliant servers.