Rebase Tools#

Configuration File: rebase_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

REBASE_get_enzyme (Type: REBASETool)#

Look up a restriction enzyme in REBASE, the reference catalogue of ~6,000 enzymes from New Englan…

REBASE_get_enzyme tool specification

Tool Information:

  • Name: REBASE_get_enzyme

  • Type: REBASETool

  • Description: Look up a restriction enzyme in REBASE, the reference catalogue of ~6,000 enzymes from New England Biolabs. Returns the recognition sequence with its cut point, whether the cut leaves blunt or sticky ends, the source organism, methylation sensitivity, commercial availability, and isoschizomers. Example: name=’EcoRI’ returns G^AATTC. The DNA_find_restriction_sites and DNA_virtual_digest calculators work from 25 curated enzymes; use this to look up anything outside that set.

Parameters:

  • name (string) (required) Enzyme name, e.g. ‘EcoRI’, ‘BamHI’, ‘SmaI’. Matched case-insensitively.

Example Usage:

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

REBASE_list_isoschizomers (Type: REBASETool)#

List every restriction enzyme sharing a prototype with the named enzyme, i.e. all enzymes with th…

REBASE_list_isoschizomers tool specification

Tool Information:

  • Name: REBASE_list_isoschizomers

  • Type: REBASETool

  • Description: List every restriction enzyme sharing a prototype with the named enzyme, i.e. all enzymes with the same recognition specificity. Commercially available enzymes are listed first, so this answers ‘which enzyme can I actually buy that cuts like this one’. Example: name=’EcoRI’.

Parameters:

  • name (string) (required) Enzyme name to find isoschizomers of, e.g. ‘EcoRI’.

Example Usage:

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

REBASE_search_by_site (Type: REBASETool)#

Find restriction enzymes by what they recognize. Give site to find every enzyme reading an exact …

REBASE_search_by_site tool specification

Tool Information:

  • Name: REBASE_search_by_site

  • Type: REBASETool

  • Description: Find restriction enzymes by what they recognize. Give site to find every enzyme reading an exact recognition sequence (site=’GAATTC’), or give sequence to find every enzyme that would cut a DNA sequence, with the number of cut sites each produces. IUPAC ambiguity codes in enzyme sites are expanded, so degenerate recognition sequences match correctly. Set only_commercial=true to restrict to enzymes you can buy.

Parameters:

  • site ([‘string’, ‘null’]) (optional) Exact recognition sequence to match, e.g. ‘GAATTC’. Mutually exclusive with sequence.

  • sequence ([‘string’, ‘null’]) (optional) DNA sequence to find cutters for, e.g. a plasmid region. Mutually exclusive with site.

  • only_commercial ([‘boolean’, ‘null’]) (optional) If true, return only commercially available enzymes.

  • limit ([‘integer’, ‘null’]) (optional) Maximum enzymes to return (default 25, max 200).

Example Usage:

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