ESPript 3.0

ESPript 3.0 visualizes multiple sequence alignments and integrates secondary-structure annotations and homology scoring to generate PostScript figures for interpretation of protein sequence and structural conservation.

Key Features:

• Integration with Sequence Alignment Programs: Accepts and visualizes alignments from CLUSTAL-W and GCG PILEUP.
• Secondary Structure Annotation: Incorporates secondary-structure information from DSSP files into alignment displays.
• Homology Scoring and Sorting: Computes homology scores for alignment columns and supports sorting by groups of sequences.
• Customizable Visualization: Provides markers and palettes to highlight and emphasize regions within alignments.
• Data Integration with Structural Files: Embeds residue conservation information into coordinate files for downstream visualization with MOLSCRIPT and CNS.
• Linkage with Other Bioinformatics Tools: Interfaces with ProDom, PredictProtein, NPS@ and ENDscript; ENDscript supports figures from PDB identifiers, structural superimposition via PROFIT, and graphical outputs via BOBSCRIPT.
• Comprehensive Output: Produces PostScript output combining multiple sequence alignments with annotated secondary-structure elements.

Scientific Applications:

• Conserved Region Identification: Visualize and identify conserved residues and motifs across homologous protein sequences.
• Evolutionary Relationship Analysis: Highlight conservation and divergence patterns to support analysis of evolutionary relationships.
• Functional Domain Annotation: Map and annotate functional domains and secondary-structure elements onto alignments and coordinate files.

Methodology:

Processes alignments from CLUSTAL-W and GCG PILEUP, reads DSSP secondary-structure files, computes column homology scores with group sorting, embeds conservation into coordinate files for MOLSCRIPT and CNS, supports structural superposition via PROFIT and rendering via BOBSCRIPT, integrates with ProDom, PredictProtein, NPS@ and ENDscript, and outputs results as PostScript figures.