Manual curation of large extrachromosomal elements (Archaea)

Knowledge graph centered on Manual curation of large extrachromosomal elements (Archaea) with 23 nodes and 64 connections. Top connected: Crested Butte, Bacteria, East River, Borgs are giant genetic elements with potential to, Archaea.

Method synopsis

Manual identification and curation of large genome fragments using GC content, coverage patterns, and taxonomic profiles to assemble complete extrachromosomal genomes.

Synthesized from method descriptions across 2 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Borgs are giant genetic elements with potential to expand metabolic capacity (2022), Nature. The protocol was originally introduced by Massive DNA "BORG" Structures Perplex Scientists (2021), Nature. Implementations in other papers (listed below) may differ.

1. Genome assembly and binning
   Assembled sequences using IDBA-UD and MEGAHIT assemblers. Performed genome binning using taxonomic profiling based on bacterial, archaeal and domain comparisons with sequence databases. Used NCBI nr database for protein annotations.
   Quantities: Generated genome bins for hundreds of contigsDuration: Not specifiedConditions: Computational analysis
   Equipment: IDBA-UD, MEGAHIT, NCBI nr database
2. Manual genome curation
   Manually curated large genome fragments to extend and join contigs with the same profile. Used GC content, coverage, and taxonomic annotation patterns to identify origins and termini of replication. Identified perfect tandem direct repeats at genome ends.
   Quantities: Four complete genomes manually curated to completion, ranging 662-918 kb in lengthDuration: Not specifiedConditions: Manual analysis
   Equipment: computational tools for sequence analysis

Typical Equipment

• IDBA-UD
• MEGAHIT
• computational tools for sequence analysis

Output Measurements

• complete genome sequences
• genome organization features

Papers Using This Protocol (2)

Species Studied With This Protocol

Places Where Used