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Slot: second ribosomal sequence (isolate_second_ribosomal_seq)

Optional secondary ribosomal sequence for additional strain verification. For 28S must be >300 nt with <10% Ns. Use only A, C, G, T, or N with no FASTA header line.

URI: nmdc_sub_schema:isolate_second_ribosomal_seq Alias: isolate_second_ribosomal_seq

Applicable Classes

Name Description Modifies Slot
JgiIsolateGenomeInterface JGI submission metadata for isolate GENOME sequencing projects yes

Properties

  • Range: String

  • Regex pattern: ^[ATCGN]{200,5000}$

Aliases

  • Second ribosomal sequence

Examples

Value
AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACT

Comments

  • Other types of ribosomal sequence may be provided as a secondary check. Sequence MUST come from the actual sample to be shipped to JGI. For 28s, the sequence must be >300 nt with <10% Ns. Please use only A, C, G, T or N, with no header.

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc_sub_schema:isolate_second_ribosomal_seq
native nmdc_sub_schema:isolate_second_ribosomal_seq

LinkML Source

name: isolate_second_ribosomal_seq
description: Optional secondary ribosomal sequence for additional strain verification.
  For 28S must be >300 nt with <10% Ns. Use only A, C, G, T, or N with no FASTA header
  line.
title: second ribosomal sequence
comments:
- Other types of ribosomal sequence may be provided as a secondary check.  Sequence
  MUST come from the actual sample to be shipped to JGI.  For 28s, the sequence must
  be >300 nt with <10% Ns. Please use only A, C, G, T or N, with no header.
examples:
- value: AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACT
from_schema: https://example.com/nmdc_submission_schema
aliases:
- Second ribosomal sequence
rank: 35
alias: isolate_second_ribosomal_seq
domain_of:
- JgiIsolateGenomeInterface
range: string
pattern: ^[ATCGN]{200,5000}$