SEQATOMS

SEQATOMS produces modified FASTA sequence entries by integrating PDB SEQRES and coordinate information and masking residues absent from the PDB coordinate section with lower-case letters to indicate missing spatial coordinates.

Key Features:

• Modified FASTA database: Generates a FASTA sequence database where residues present in SEQRES but absent from the PDB coordinate section are represented with lower-case letters.
• Lower-case masking: Marks residues lacking three-dimensional coordinates using lower-case letters to distinguish them from residues with known coordinates.
• Case-sensitive BLAST: Provides BLAST-based similarity searches that preserve case, allowing masked (lower-case) regions to remain visible in search results.
• Masked CATH database: Produces a masked version of the CATH domain database with the same lower-case masking applied to residues missing coordinates.
• Identification of sequence-structure gaps: Enables identification and contextual inspection of sequence regions that lack corresponding coordinate data in PDB entries.

Scientific Applications:

• Mapping sequence-structure gaps: Detects and annotates residues present in SEQRES but missing from coordinate data to map gaps between sequence and structure.
• Similarity searches distinguishing coordinate availability: Uses case-sensitive BLAST results to distinguish residues with known versus unknown spatial positions in comparative analyses.
• Assessment of PDB completeness: Assists in evaluating the completeness and coverage of structural data in PDB entries.
• CATH domain analyses with masked residues: Facilitates analyses of CATH domains while explicitly marking residues lacking coordinate information.

Methodology:

Integrates PDB SEQRES and coordinate data to produce modified FASTA sequences with residues absent from the coordinate section masked as lower-case; implements a case-sensitive BLAST search that preserves case in results; generates a masked CATH domain database.