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Term: similarity search method (sim_search_meth)

Tool used to compare ORFs with database, along with version and cutoffs used

URI: MIXS:0000063

Applicable Checklists and Extensions

NOTE: does not include Combinations (of checklists and extensions) that use sim_search_meth.

Name Description Checklist/Extension
MigsVi Minimal Information about a Genome Sequence: virus Checklist
MigsOrg Minimal Information about a Genome Sequence: organelle Checklist
Mimag Minimum Information About a Metagenome-Assembled Genome Checklist
Miuvig Minimum Information About an Uncultivated Virus Genome Checklist
MigsPl Minimal Information about a Genome Sequence: plasmid Checklist
Mims Metagenome or Environmental Checklist
Misag Minimum Information About a Single Amplified Genome Checklist
MigsEu Minimal Information about a Genome Sequence: eukaryote Checklist
MigsBa Minimal Information about a Genome Sequence: cultured bacteria/archaea Checklist

Properties

  • Range: String
  • Cardinality: 0..1

  • Structured pattern: ^{software};{version};{parameters}$

  • Regex pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$

Examples

Value
HMMER3;3.1b2;hmmsearch, cutoff of 50 on score

LinkML Source

name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
  used
title: similarity search method
examples:
- value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000063
alias: sim_search_meth
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
  syntax: ^{software};{version};{parameters}$
  interpolated: true
  partial_match: true