Database link : https://www.ncbi.nlm.nih.gov/refseq/targetedloci/

NCBI RefSeq Targeted Loci Project

Targeted loci are specific molecular markers such as protein coding or ribosomal RNA loci (16S rDNA, 18S rDNA (SSU), 28S rDNA (LSU) gene and internal transcribed spacer (ITS)) that are used for phylogenetic and barcoding analysis.
SCOPE

Targeted loci currently include genic and spacer regions of the nuclear ribosomal cistron. The scope includes curated RefSeq records (NCBI RefSeq Targeted Loci projects) and selected validated GenBank sequences for curated BLAST databases. RefSeq records are available for Archaea, Bacteria and Fungi which are accessible via Entrez query and BLAST search interfaces. Selected validated GenBank sequences are accessible via BLAST search interfaces and are available for Animals, Plants and Protists.
BLAST DATABASES

REFSEQ records (Archaea, Bacteria and Fungi)

    REFSEQ BLAST Search against curated RefSeq records from ribosomal RNA loci. Select "Sequences from type material" to limit your search to type only. See RefSeq project descriptions below for more curation detail of the source.

    MOLE-BLAST A tool that helps users find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results.
SELECTED GENBANK sequences (Animals, Plants and Protists)

    SELECTED GENBANK BLAST Search against selected GenBank sequences from ribosomal RNA loci. The validation procedure of 18S and 28S rDNA sequences included the ribodbmaker pipeline (part of the ribovore package), available at https://github.com/nawrockie/ribovore). Ribodbmaker compares sequences against rRNA Rfam models (RF01960 (SSU) and RF02543 (LSU)) to: validate eukaryotic origin and rRNA continuity; identify potentially misassembled sequences; verify unexpectedly divergent sequences relative to other eukaryotic sequences of its rank. The pipeline also removes sequences with: too many ambiguous nucleotides, vector subsequences recognized by VecScreen, and repeated subsequences that are indicative of missassembly. Verification of the ITS region in ITS sequences included the ITSx program available at https://microbiology.se/software/itsx/. Additionally sequences were checked for too many ambiguous nucleotides and vector subsequences recognized by VecScreen.

REFSEQ TARGETED LOCI PROJECTS

Archaea FTP: ftp://ftp.ncbi.nlm.nih.gov/refseq/TargetedLoci/Archaea/

Bacteria FTP: ftp://ftp.ncbi.nlm.nih.gov/refseq/TargetedLoci/Bacteria/

Bacteria and Archaea: 16S ribosomal RNA project

    The small subunit ribosomal RNA is a useful phylogenetic marker that has been used extensively for evolutionary analyses. The RefSeq dataset contains curated 16S ribosomal RNA sequences that correspond to bacteria and archaea type materials. The RefSeq records may contain corrections to the sequence or taxonomy as compared to the original INSD submission, and may have additional information added that is not found in the original. See more details on curation process.
    16S RefSeq Nucleotide sequence records

Number of sequence / taxon:
- NCBIdb_archaea_16S_v1.20230726:
    - 1130 sequences
    - 1 Kingdom
    - 5 Phyla
    - 13 Classes
    - 25 Orders
    - 43 Families
    - 161 Genera
    - 645 Species
- NCBIdb_bacteria_16S_v1.20230726:
    - 25849 sequences
    - 2 Kingdom (Bacteria and Unassigned)
    - 45 Phyla
    - 118 Classes
    - 259 Orders
    - 694 Families
    - 3929 Genera
    - 19621 Species