Ebi Sequence Tools#

Configuration File: ebi_sequence_tools.json Tool Type: Local Tools Count: 5

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

Available Tools#

EBI_pairwise_align (Type: EBIPairwiseAlignTool)#

Align exactly two sequences via EMBL-EBI EMBOSS and return the alignment with percent identity, s…

EBI_pairwise_align tool specification

Tool Information:

  • Name: EBI_pairwise_align

  • Type: EBIPairwiseAlignTool

  • Description: Align exactly two sequences via EMBL-EBI EMBOSS and return the alignment with percent identity, similarity, gaps, and score. Choose algorithm=’needle’ for Needleman-Wunsch global alignment (default), ‘stretcher’ for memory-efficient global alignment of long sequences, or ‘matcher’ for Smith-Waterman local alignment. Use EBI_msa_align instead when aligning three or more sequences. Jobs are submitted and polled, so a call takes several seconds.

Parameters:

  • sequence_a (string) (required) First sequence, FASTA or raw.

  • sequence_b (string) (required) Second sequence, FASTA or raw.

  • algorithm ([‘string’, ‘null’]) (optional) ‘needle’ (global, default), ‘stretcher’ (global, long sequences), or ‘matcher’ (local).

  • sequence_type ([‘string’, ‘null’]) (optional) ‘protein’ (default) or ‘dna’.

  • matrix ([‘string’, ‘null’]) (optional) Scoring matrix, e.g. ‘EBLOSUM62’ for protein or ‘EDNAFULL’ for DNA.

  • gap_open ([‘number’, ‘null’]) (optional) Gap opening penalty.

  • gap_extend ([‘number’, ‘null’]) (optional) Gap extension penalty.

Example Usage:

query = {
    "name": "EBI_pairwise_align",
    "arguments": {
        "sequence_a": "example_value",
        "sequence_b": "example_value"
    }
}
result = tu.run(query)

EBI_predict_membrane_topology (Type: EBIPhobiusTool)#

Predict transmembrane helices and signal peptides from a protein sequence using Phobius via EMBL-…

EBI_predict_membrane_topology tool specification

Tool Information:

  • Name: EBI_predict_membrane_topology

  • Type: EBIPhobiusTool

  • Description: Predict transmembrane helices and signal peptides from a protein sequence using Phobius via EMBL-EBI. Returns the helix count, whether a signal peptide is predicted, and per-feature coordinates (TRANSMEM, SIGNAL, DOMAIN with inside/outside orientation). This is a sequence-based prediction; for experimentally derived topology of solved structures use structure resources instead. Jobs are submitted and polled, so a call takes several seconds.

Parameters:

  • sequence (string) (required) Protein sequence, FASTA or raw.

Example Usage:

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

EBI_profile_search (Type: EBIProfileSearchTool)#

Search a protein sequence against a sequence database using a profile method via EMBL-EBI: method…

EBI_profile_search tool specification

Tool Information:

  • Name: EBI_profile_search

  • Type: EBIProfileSearchTool

  • Description: Search a protein sequence against a sequence database using a profile method via EMBL-EBI: method=’phmmer’ (HMMER3, default) or ‘psiblast’ (iterative PSI-BLAST). Profile methods detect remote homologs that a single-pass BLAST misses. Valid databases differ by method: phmmer accepts swissprot, uniprotkb, uniprotrefprot, rp75, rp55, rp15; psiblast accepts uniprotkb, uniprotkb_swissprot, uniprotkb_reference_proteomes. Jobs are submitted and polled, so a call takes several seconds.

Parameters:

  • sequence (string) (required) Protein sequence, FASTA or raw.

  • method ([‘string’, ‘null’]) (optional) ‘phmmer’ (default) or ‘psiblast’.

  • database ([‘string’, ‘null’]) (optional) Target database; valid values depend on method. Defaults to swissprot for phmmer, uniprotkb for psiblast.

  • evalue ([‘number’, ‘null’]) (optional) E-value threshold, e.g. 0.001.

Example Usage:

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

EBI_scan_pfam_domains (Type: EBIPfamScanTool)#

Scan a protein sequence against Pfam HMMs via EMBL-EBI PfamScan and return each matched domain wi…

EBI_scan_pfam_domains tool specification

Tool Information:

  • Name: EBI_scan_pfam_domains

  • Type: EBIPfamScanTool

  • Description: Scan a protein sequence against Pfam HMMs via EMBL-EBI PfamScan and return each matched domain with its coordinates, Pfam accession, bit score, E-value, and significance flag. Faster and Pfam-specific compared with InterProScan_scan_sequence, which searches many member databases; use InterProScan when you need the full signature set. Jobs are submitted and polled, so a call takes several seconds.

Parameters:

  • sequence (string) (required) Protein sequence, FASTA or raw.

  • database ([‘string’, ‘null’]) (optional) ‘pfam-a’ (default).

  • evalue ([‘number’, ‘null’]) (optional) E-value cutoff, e.g. 0.001.

Example Usage:

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

EBI_translate_sequence (Type: EBITranslateSequenceTool)#

Translate nucleotide to protein, back-translate protein to nucleotide, or produce a six-frame tra…

EBI_translate_sequence tool specification

Tool Information:

  • Name: EBI_translate_sequence

  • Type: EBITranslateSequenceTool

  • Description: Translate nucleotide to protein, back-translate protein to nucleotide, or produce a six-frame translation with ORF detection, via EMBL-EBI EMBOSS. Set mode=’dna_to_protein’ (default, transeq), ‘protein_to_dna’ (backtranseq), or ‘six_frame’ (sixpack). Supports alternative genetic codes through codon_table. Complements the local DNA_* helpers by handling alternative codon tables and six-frame ORF calling server-side.

Parameters:

  • sequence (string) (required) Input sequence, FASTA or raw.

  • mode ([‘string’, ‘null’]) (optional) ‘dna_to_protein’ (default), ‘protein_to_dna’, or ‘six_frame’.

  • frame ([‘string’, ‘null’]) (optional) Reading frame for dna_to_protein: ‘1’,’2’,’3’,’-1’,’-2’,’-3’, or ‘6’ for all.

  • codon_table ([‘string’, ‘null’]) (optional) Genetic code, e.g. ‘0’ standard, ‘2’ vertebrate mitochondrial, ‘11’ bacterial.

  • min_orf_size ([‘integer’, ‘null’]) (optional) Minimum ORF size in nucleotides for six_frame mode.

Example Usage:

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