Sequence Analyze Tools#

Configuration File: sequence_analyze_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the sequence_analyze_tools.json configuration file.

Available Tools#

Sequence_count_residues (Type: SequenceAnalyzeTool)#

Count occurrences of a specific amino acid or nucleotide residue in a sequence. Accepts either a …

Sequence_count_residues tool specification

Tool Information:

  • Name: Sequence_count_residues

  • Type: SequenceAnalyzeTool

  • Description: Count occurrences of a specific amino acid or nucleotide residue in a sequence. Accepts either a raw sequence string or a UniProt accession (fetches protein sequence from UniProt REST API). Reports count, fraction, percentage, and pageable 1-based positions, including explicit truncation and continuation fields for residues occurring more than 50 times.

Parameters:

  • operation (string) (optional) Operation type

  • sequence (string) (optional) Sequence string (DNA/RNA/protein). Optional if uniprot_id is provided.

  • uniprot_id (string) (optional) UniProt accession to fetch sequence from (e.g., ‘P00533’ for EGFR). Optional if sequence is provided.

  • residue (string) (required) Single character residue to count (e.g., ‘C’ for cysteine)

  • position_limit (integer) (optional) Maximum number of matching 1-based residue positions to return on this page.

  • position_offset (integer) (optional) Zero-based offset into all matching residue positions. Continue with data.next_position_offset while data.positions_truncated is true.

Example Usage:

query = {
    "name": "Sequence_count_residues",
    "arguments": {
        "residue": "example_value"
    }
}
result = tu.run(query)

Sequence_gc_content (Type: SequenceAnalyzeTool)#

Calculate GC content of a DNA or RNA sequence. Reports GC count, GC fraction, GC percentage, and …

Sequence_gc_content tool specification

Tool Information:

  • Name: Sequence_gc_content

  • Type: SequenceAnalyzeTool

  • Description: Calculate GC content of a DNA or RNA sequence. Reports GC count, GC fraction, GC percentage, and full nucleotide composition. Ambiguous bases (N) are excluded from the denominator. Useful for primer design, genome characterization, and codon usage analysis.

Parameters:

  • operation (string) (optional) Operation type

  • sequence (string) (required) DNA or RNA sequence string

Example Usage:

query = {
    "name": "Sequence_gc_content",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

Sequence_reverse_complement (Type: SequenceAnalyzeTool)#

Return the reverse complement of a DNA sequence. Supports A, T, C, G, and N bases. Useful for pri…

Sequence_reverse_complement tool specification

Tool Information:

  • Name: Sequence_reverse_complement

  • Type: SequenceAnalyzeTool

  • Description: Return the reverse complement of a DNA sequence. Supports A, T, C, G, and N bases. Useful for primer design, probe design, and strand orientation analysis.

Parameters:

  • operation (string) (optional) Operation type

  • sequence (string) (required) DNA sequence (A/T/C/G/N only)

Example Usage:

query = {
    "name": "Sequence_reverse_complement",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

Sequence_stats (Type: SequenceAnalyzeTool)#

Compute basic statistics for a DNA, RNA, or protein sequence. Auto-detects sequence type, reports…

Sequence_stats tool specification

Tool Information:

  • Name: Sequence_stats

  • Type: SequenceAnalyzeTool

  • Description: Compute basic statistics for a DNA, RNA, or protein sequence. Auto-detects sequence type, reports length, full composition, and type-specific metrics (GC% for nucleotides, estimated monoisotopic molecular weight for proteins – for the conventional average mass reported by ExPASy ProtParam/UniProt, use ProtParam_calculate instead). Accepts sequence string or UniProt accession.

Parameters:

  • operation (string) (optional) Operation type

  • sequence (string) (optional) Sequence string. Optional if uniprot_id is provided.

  • uniprot_id (string) (optional) UniProt accession to fetch protein sequence from. Optional if sequence is provided.

Example Usage:

query = {
    "name": "Sequence_stats",
    "arguments": {
    }
}
result = tu.run(query)