16S rRNA RefSeq: V15.23    Genomic RefSeq: V10.1
Download HOMD Data
Genomic Meta Information::Batch Downloads
TypeFormats
Sequence Meta Information [page]Tab Delimited Text
(View in browser)		Tab Delimited Text
(Save to file)		MS Excel Format
(Save to file)
NCBI Genome Annotations[FTP Site for download]
PROKKA Genome Annotations[FTP Site for download]
Genomic Trees:
Conserved Protein, Ribosomal Protein and 16S rRNA		[FTP Site for download]
Phylogenetics
TypeFormats
Phylogenetic tree of HOMD 16S rRNA Reference Sequences svg newick Sequence ID table
Phylogenetic tree of 16S rRNA gene sequences identified in HOMD genomes svg newick Sequence ID table
Phylogenomic tree based on conserved proteins identified from HOMD genomes svg newick Sequence ID table
Phylogenetic tree of ribosomal proteins identified from HOMD genomes svg newick Sequence ID table
Download HOMD 16S rRNA Gene Sequences
HOMD provides two different sets of 16S rRNA Gene Reference Sequence (RefSeq) for download and BLAST search: 

  1. HOMD 16S rRNA RefSeq: This set contains sequences representing all currently named and unnamed oral taxa.
  2. HOMD 16S rRNA Extended RefSeq: This set contains additional16S rRNA reference gene sequences that are 
      distinctively different from existing taxa but have not yet been assigned with a taxon ID.
A phylogeny-based, high-resolution, habitat-specific training reference sequence set was constructed to achieve species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived amplicon sequence variants (ASVs). The training set sequences, together with the pipeline scripts, are available for download. For detail description of the training set and the pipelines, please refer to our publication Escapa et al, 2020.

In addition, the entire collection of all cloned sequences (clonal collection) upon which the Refseq was derived from, is also provided for download on this page and on the HOMD FTP site.
[View Version History]
Date Version Name
HOMD 16S rRNA RefSeq *Right-click to download
or click to open
2023-04-10eHOMD 16S rRNA RefSeq Version 15.23 (Starts from position 28) [Download]
2023-04-10eHOMD 16S rRNA RefSeq Version 15.23 (Starts from position 9) [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.22 (Starts from position 28) [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.22 (Starts from position 9) [Download]
2017-11-16eHOMD 16S rRNA RefSeq Version 15.1 (Starts from position 28) [Download]
2017-11-16eHOMD 16S rRNA RefSeq Version 15.1 (Starts from position 9) [Download]
2017-01-03HOMD 16S rRNA RefSeq Version 14.51 (Starts from position 28) [Download]
2017-01-03HOMD 16S rRNA RefSeq Version 14.51 (Starts from position 9) [Download]
2016-03-29HOMD 16S rRNA RefSeq Version 14.5 (Starts from position 28) [Download]
2016-03-29HOMD 16S rRNA RefSeq Version 14.5 (Starts from position 9) [Download]
2013-05-08HOMD 16S rRNA RefSeq Version 13.2 (Starts at position 28) [Download]
2013-05-08HOMD 16S rRNA RefSeq Version 13.2 (Starts at position 9) [Download]
2013-03-25HOMD 16S rRNA RefSeq Version 13.0 [Download]
2013-01-16HOMD 16S rRNA RefSeq Version 12.0 [Download]
2012-02-16HOMD 16S rRNA RefSeq Version 11.0 [Download]
2010-02-08HOMD 16S rRNA RefSeq Version 10.1 [Download]
2009-02-03HOMD 16S rRNA RefSeq Version 10 [Download]
HOMD 16S rRNA Extended RefSeq *
2010-02-19HOMD 16S rRNA RefSeq Extended Version 1.1 [Download]
2009-02-25HOMD 16S rRNA RefSeq Extended Version 1 [Download]
HOMD 16S rRNA Gene Sequence Clonal Collection
2010-02-07HOMD 16S rRNA Gene Sequence Clonal Collection Version 1 [Download]
eHOMD 16S rRNA training sequence sets
2018-12-03eHOMD 16S rRNA full-length training set [Download]
2018-12-03eHOMD 16S rRNA V1V3 training set [Download]
Other training set related files [link to FTP site] [Link Out]
Other Download Formats
2021-02-09eHOMD 16S rRNA RefSeq Version 15.23 Aligned FASTA File [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.23 Taxonomy File for MOTHUR [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.23 Taxonomy File for QIIME [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.22 Aligned FASTA File [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.22 Taxonomy File for MOTHUR [Download]
2021-02-09eHOMD 16S rRNA RefSeq Version 15.22 Taxonomy File for QIIME [Download]
2017-11-16eHOMD 16S rRNA RefSeq Version 15.1 Aligned FASTA File [Download]
2017-11-16eHOMD 16S rRNA RefSeq Version 15.1 Taxonomy File for MOTHUR [Download]
2017-11-16eHOMD 16S rRNA RefSeq Version 15.1 Taxonomy File for QIIME [Download]
2017-01-03HOMD 16S rRNA RefSeq Version 14.51 Aligned FASTA File [Download]
2017-01-03HOMD 16S rRNA RefSeq Version 14.51 Taxonomy File for MOTHUR [Download]
2017-01-03HOMD 16S rRNA RefSeq Version 14.51 Taxonomy File for QIIME [Download]
2016-03-29HOMD 16S rRNA RefSeq Version 14.5 Aligned FASTA File [Download]
2016-03-29HOMD 16S rRNA RefSeq Version 14.5 Taxonomy File for MOTHUR [Download]
2016-03-29HOMD 16S rRNA RefSeq Version 14.5 Taxonomy File for QIIME [Download]
2013-05-08HOMD 16S rRNA RefSeq Version 13.2 Aligned FASTA File [Download]
2013-05-08HOMD 16S rRNA RefSeq Version 13.2 FASTA File in QIIME Format [Download]
2014-09-11HOMD 16S rRNA RefSeq Version 13.2 FASTA File for mothur [Download]
2014-09-11HOMD 16S rRNA RefSeq Version 13.2 Taxonomy File for mothur [Download]
* These sequences are corrected consensus sequences. Many have been corrected and extended based on alignment with other sequences for that taxon and Ns and indels removed. Therefore, for many sequences, there will be differences between the Reference Sequence and the GenBank sequence listed in the header information. We have not yet updated our own GenBank sequences, and can not update those from other depositors. We believe these are currently the best reference sequences available, and for the purposes of BLAST analysis, have the advantage of being of a uniform length.
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