showalign

showalign displays multiple sequence alignments to visualize and compare nucleotide and protein sequence similarities and differences for molecular biology analyses.

Key Features:

• EMBOSS integration: Implemented as part of the European Molecular Biology Open Software Suite (EMBOSS) and interoperable with the suite's applications and third-party tools, including the broader set of over 200 EMBOSS programs.
• Alignment visualization: Renders multiple sequence alignments in an organized, columnar format that highlights conserved and variable positions across sequences.
• Customization via ACD files: Supports customization and development of application behavior through Application Configuration Description (ACD) files.
• C library foundation: Leverages EMBOSS C programming libraries for sequence handling and internal data structures.

Scientific Applications:

• Sequence alignment visualization: Presents multiple sequence alignments to facilitate inspection of conserved residues and indels across sequences.
• Phylogenetic analysis support: Provides alignment outputs used as input for phylogenetic inference and evolutionary relationship studies.
• Gene annotation and comparative genomics: Aids comparison of homologous regions for gene annotation and comparative genomic analyses.
• Protein structure prediction support: Supplies alignment-derived conservation information useful for protein structure and function prediction.
• Functional genomics: Enables visualization of sequence variation and conservation relevant to functional genomics investigations.

Methodology:

Operates within the EMBOSS framework using EMBOSS C programming libraries and accepts customization via Application Configuration Description (ACD) files.