GGGenome | ultrafast DNA search

GGGenome is an ultrafast search engine for nucleotide sequences.
Freely available to all users.
Searches are always case insensitive.
U and T will be treated identically.
Ambiguous nucleotide characters (N, R, Y ...) can be used.
All other characters are ignored.
GGGenome shows 50 hits per page.
Maximum 100000 hits can be retrieved as TXT, CSV, BED, GFF or JSON format.

GGGenome search using Google Spreadsheet.

Search genes and transcripts by various keywords → Please try
- Example for searching 'nanog' in human: https://GGRNA.dbcls.jp/hs/nanog

Tutorial video introducing GGGenome

URIs

http[s]://GGGenome.dbcls.jp/db/k/[strand]/[nogap]/sequence[.format][.download]
- db: hg38, mm10, dm3, ce10, TAIR10, pombe, refseq, etc. (default: hg38)
  Full list of databases is available below.
- k: Maximum number of mismatches/gaps. (default: 0)
- strand: '+' ('plus') or '-' ('minus') to search specified strand only. (optional)
- nogap: No gaps. Allow only k mismatches. (optional)
- sequence: Nucleotide sequence, case insensitive.
- format: html, txt, csv, bed, gff, json. (default: html)
- download: Download result as a file. (optional)
Example 1: https://GGGenome.dbcls.jp/TTCATTGACAACATT
- Search TTCATTGACAACATT in
- human genome hg38 (default),
- with perfect matches (default),
- output in html format (default).
Example 2: https://GGGenome.dbcls.jp/mm10/2/+/nogap/TTCATTGACAACATTGCGT.txt
- Search TTCATTGACAACATTGCGT in
- mouse genome mm10,
- allowing 2 mismatches,
- search for + strand only,
- with nogap (allow only mismatches),
- output in tab-delimited txt format.

List of databases (Genome)

Show entries

Search:

Database	Source	Group	Species	Latin name	Assembly information
hg38	UCSC	Mammal	Human	Homo sapiens	GRCh38/hg38 (Dec, 2013)
hg19	UCSC	Mammal	Human	Homo sapiens	GRCh37/hg19 (Feb, 2009)
hg18	UCSC	Mammal	Human	Homo sapiens	NCBI36/hg18 (Mar, 2006)
mm39	UCSC	Mammal	Mouse	Mus musculus	GRCm39/mm39 (Jun, 2020)
mm10	UCSC	Mammal	Mouse	Mus musculus	GRCm38/mm10 (Dec, 2011)
mm9	UCSC	Mammal	Mouse	Mus musculus	NCBI37/mm9 (Jul, 2007)
rn6	UCSC	Mammal	Rat	Rattus norvegicus	RGSC 6.0/rn6 (Jul, 2014)
rn5	UCSC	Mammal	Rat	Rattus norvegicus	RGSC 5.0/rn5 (Mar, 2012)
vicPac2	UCSC	Mammal	Alpaca	Vicugna pacos	Vicugna_pacos-2.0.1/vicPac2 (Mar, 2013)
dasNov3	UCSC	Mammal	Armadillo	Dasypus novemcinctus	Baylor/dasNov3 (Dec, 2011)
papAnu2	UCSC	Mammal	Baboon	Papio anubis	Baylor Panu_2.0/papAnu2 (Mar, 2012)
bisBis1	UCSC	Mammal	American bison	Bison bison	Bison_UMD1.0/bisBis1 (Oct, 2014)
panPan2	UCSC	Mammal	Bonobo	Pan paniscus	MPI-EVA panpan1.1/panPan2 (Aug, 2015)
otoGar3	UCSC	Mammal	Bushbaby	Otolemur garnettii	Broad/otoGar3 (Mar, 2011)
felCat8	UCSC	Mammal	Cat	Felis catus	ICGSC Felis_catus_8.0/felCat8 (Nov, 2014)
felCat5	UCSC	Mammal	Cat	Felis catus	ICGSC Felis_catus 6.2/felCat5 (Sep, 2011)
panTro5	UCSC	Mammal	Chimpanzee	Pan troglodytes	Pan_tro 3.0/panTro5 (May, 2016)
panTro4	UCSC	Mammal	Chimpanzee	Pan troglodytes	CSAC 2.1.4/panTro4 (Feb, 2011)
criGri1	UCSC	Mammal	Chinese hamster	Cricetulus griseus	C_griseus_v1.0/criGri1 (Jul, 2013)
manPen1	UCSC	Mammal	Chinese pangolin	Manis pentadactyla	M_pentadactyla-1.1.1/manPen1 (Aug, 2014)
bosTau8	UCSC	Mammal	Cow	Bos taurus	Bos_taurus_UMD_3.1.1/bosTau8 (Jun, 2014)
bosTau7	UCSC	Mammal	Cow	Bos taurus	Btau_4.6.1/bosTau7 (Oct, 2011)
macFas5	UCSC	Mammal	Crab-eating macaque	Macaca fascicularis	Macaca_fascicularis_5.0/macFas5 (Jun, 2013)
canFam3	UCSC	Mammal	Dog	Canis familiaris	Broad CanFam3.1/canFam3 (Sep, 2011)
turTru2	UCSC	Mammal	Dolphin	Tursiops truncatus	Baylor Ttru_1.4/turTru2 (Oct, 2011)

Showing 1 to 25 of 749 entries

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List of databases (Others)

Show entries

Search:

Database	Source	Group	Species	Latin name	Definition
refseq (alias of latest release) refseq228	RefSeq				RefSeq complete RNA release 228 (Jan, 2025)
refseq227	RefSeq				RefSeq complete RNA release 227 (Nov, 2024)
refseq225	RefSeq				RefSeq complete RNA release 225 (Jul, 2024)
refseq220	RefSeq				RefSeq complete RNA release 220 (Sep, 2023)
refseq215	RefSeq				RefSeq complete RNA release 215 (Nov, 2022)
refseq210	RefSeq				RefSeq complete RNA release 210 (Jan, 2022)
refseq205	RefSeq				RefSeq complete RNA release 205 (Mar, 2021)
refseq200	RefSeq				RefSeq complete RNA release 200 (May, 2020)
refseq90	RefSeq				RefSeq complete RNA release 90 (Sep, 2018)
refseq80	RefSeq				RefSeq complete RNA release 80 (Jan, 2017)
refseq70	RefSeq				RefSeq complete RNA release 70 (May, 2015)
hs_refseq225	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA release 225 (Jul, 2024)
hsnm_refseq225	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (NM/NR) release 225 (Jul, 2024)
hsxm_refseq225	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (XM/XR) release 225 (Jul, 2024)
hs_refseq220	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA release 220 (Sep, 2023)
hsnm_refseq220	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (NM/NR) release 220 (Sep, 2023)
hsxm_refseq220	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (XM/XR) release 220 (Sep, 2023)
hs_refseq215	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA release 215 (Nov, 2022)
hsnm_refseq215	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (NM/NR) release 215 (Nov, 2022)
hsxm_refseq215	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (XM/XR) release 215 (Nov, 2022)
hs_refseq210	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA release 210 (Jan, 2022)
hsnm_refseq210	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (NM/NR) release 210 (Jan, 2022)
hsxm_refseq210	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (XM/XR) release 210 (Jan, 2022)
hs_refseq205	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA release 205 (Mar, 2021)
hsnm_refseq205	RefSeq	Mammal	Human	Homo sapiens	RefSeq human RNA (NM/NR) release 205 (Mar, 2021)

Showing 1 to 25 of 252 entries

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Search example

Search tips

Tutorial video introducing GGGenome

URIs

List of databases (Genome)

List of databases (Others)

Reference

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