• GGRNA is a Google-like search engine for genes and transcripts archived in NCBI RefSeq.
• Freely available to all users.
• RefSeq includes genomic, mRNA, noncoding RNA (ncRNA), and protein records.
  Of these, GGRNA searches for RefSeq mRNA (accession starts with NM_/XM_) and ncRNA (NR_/XR_) records.
  FTP: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete/complete.*.rna.gbff.gz
• Search is always case insensitive.
• Search for a phrase by enclosing it in double quotes (e.g. "PAZ domain").
• GGRNA will find results that contain all the terms separated by spaces or commas.
• Word order does not affect search results.
• Advanced search is available for refining your query.
• Instead, you can refine your query by using operators (see below: shown in green).
• Search genomic sequence → Please try
  • Example for searching human genome: https://GGGenome.dbcls.jp/TTCATTGACAACATT

• Nucleotide sequences
• Amino-acid sequences

Acknowledgement: We thank Mr. Masamichi Chichii for making the tutorial video on TogoTV.

Search words	Description	Alias
refid:NM_001518	Search by RefSeq ID. Version number following a dot is ignored: [ refid:NM_003380.2 ] and [ refid:NM_003380 ] will return the same results. Words starting with NM_, XM_, NR_, or XR_ is automatically treated as refid: search without operator.	refseqid: refseq: id:NM_ id:XM_ id:NR_ id:XR_
geneid:10579	Search by Gene ID. An integer is automatically treated as geneid: search without operator.	gene:integer id:integer
symbol:VIM	Search for gene symbols and synonyms which partially match to the query. For example, query EIF2C will return EIF2C1, 2, 3, and 4.	name: gene:word
aa:KDEL	Search for amino acid sequence.
ref:Naito ref:1327585	Full text search within cited references. PubMed ID can also be queried.	reference:
probe:1552311_a_at probe:A_23_P101434	Search for nucleotide sequences by microarray probe ID. Words ending with _at, _st (Affymetrix ID) and starting with A_ (Agilent ID) are automatically treated as probe: search without operator. When probe ID is not converted into sequences, the probe ID is subjected to a basic search.	probeid:
seq:caagaagagattg	Search for nucleotide sequence. Query containing letters A,T,G,C, and U only will automatically be treated as seq: search without the operator. U and T will be treated identically. seq1:, seq2:, and seq3: will return results with 1-, 2-, and 3-nucleotides mismatch tolerance.	sequence:
comp:caagaagagattg	Search for complementary sequence. comp1:, comp2:, and comp3: will return results with 1-, 2-, and 3-nucleotides mismatch tolerance.	complementary:
both:caagaagagattg	Simultaneously retrieve sense and antisense nucleotide sequences corresponding to the query. both1:, both2:, and both3: will return results with 1-, 2-, and 3-nucleotides mismatch tolerance.	bothseq:
iub:aggtcannrtgacct iubcomp:aggtcannrtgacct iubboth:aggtcannrtgacct	Search for nucleotide sequence containing IUB code letters (i.e. N, R, Y, ...). iubcomp: will return complementary sequences to the query; iubboth: will return both strands.	iubseq: → iub:

• Please use GGGenome for searching nucleotide sequences with mismatches and gaps.

• http[s]://GGRNA.dbcls.jp/species/query+string[.format][.download]
  • species → hs for Homo sapiens, mm for Mus musculus, etc. default: zoo (all species in RefSeq)
  • query+string → a simple keyword or a URL-encoded string.
  • format → html, txt, json as output format. (default: html)
  • download → download result as a file. (optional)
• Currently available species and format types are listed here:
  • https://GGRNA.dbcls.jp/api.txt
• Examples:
  • https://GGRNA.dbcls.jp/NM_001518.txt
    (Search "NM_001518". Output in tab delimited text format.)
  • https://GGRNA.dbcls.jp/mm/homeobox.txt
    (Search "homeobox" in mouse. Output in tab delimited text format.)
  • https://GGRNA.dbcls.jp/dm/%22RNA+interference%22.json
    (Search "RNA interference" in D. melanogaster. Output in JSON format.
    Note that a double quote is encoded as %22, and a space character is encoded as + in the URL.)
  • https://GGRNA.dbcls.jp/caagaagagattg.json
    (Search "caagaagagattg" in all species. Output in JSON format.)

• GGRNA searches for all species in RefSeq by default.
• However, 13 species listed below can be searched separately from following URLs.

Human (hs)	Mouse (mm)	Rat (rn)	Chicken (gg)
Frog (xt)	Zebrafish (dr)	Sea squirt (ci)	Fly (dm)
Worm (ce)	Arabidopsis (at)	Rice (os)
S. cerevisiae (sc)	S. pombe (sp)

If you use GGRNA in your work, please cite GGRNA paper.

• Yuki Naito & Hidemasa Bono (2012)
  GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
  Nucleic Acids Res. 40, W592-W596.
• Source code: GitHub - meso-cacase/GGRNA

• GitHub Wiki - GGRNA news archive