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GGGenome

GGGenome is a ultrafast DNA sequence search service hosted by Database Center for Life Science (DBCLS). See "GGGenome Help" (https://gggenome.dbcls.jp/en/help.html) for more details.

BioServices.GGGenome is a Julia module interfaces with the GGGenome REST API to query a DNA sequence to various databases programmatically.

Getting Started

Import module:

using BioServices.GGGenome

Method's documentation

Retrieve results of gggenome search of a query sequence.

# BioServices.GGGenome.gggsearch — Method.

gggsearch(query::AbstractString; 
          db="hg19", k=0, strand=nothing, 
          format="html", timeout=5, 
          output=nothing, show_url=false)

Retrieve results of gggenome search of a query sequence.

Arguments

Required

  • query::String: Nucleotide sequence, case insensitive.

Optional

  • db::String: Target database name. hg19 if not specified. Full list of databases: https://gggenome.dbcls.jp/en/help.html#db_list
  • k::Integer: Maximum number of mismatches/gaps. 0 if not specified.
  • strand::String: '+' ('plus') or '-' ('minus') to search specified strand only.
  • format::String: [html|txt|csv|bed|gff|json]. html if not specified.
  • timeout::Real: Maximum time allowed for a query.
  • output::String: If "toString", a String object is returned. If "extractTopHit", a String object containing only top hit is returned (Currently, only works with format="txt"). Otherwise, a HTTP.Messages.Response object is returned.
  • show_url::Bool: If true, print URL of REST API.

source

Retrieve full list of available databases

# BioServices.GGGenome.gggdbs — Method.

gggdbs()

Retrieve full list of available databases. Full list of databases: https://gggenome.dbcls.jp/en/help.html#db_list.

source

Available Databases

Genome sequences (hg19, mm10, dm3, ce10, TAIR10, pombe, etc.) and other sequence databases (e.g., refseq) are available.

Full list of available databases is https://gggenome.dbcls.jp/en/mm10/help.html#db_list.

Examples

Example 1

  • Search TTCATTGACAACATT in
  • human genome hg19 (default),
  • with perfect matches (default),
  • in json format.
julia> res = gggsearch("TTCATTGACAACATT", format="bed", output="toString");

julia> print(res)
track name=GGGenome description="GGGenome matches"
chr1    83462475        83462490        .       0       +
chr2    161223114       161223129       .       0       +
chr3    15289789        15289804        .       0       +
chr3    84619844        84619859        .       0       +
....

Example 2

  • Search TTCATTGACAACATTGCGT in
  • mouse genome mm10,
  • allowing 2 mismatches/gaps,
  • search for + strand only,
  • in tab-delimited txt format.
julia> res = gggsearch("TTCATTGACAACATTGCGT", db="mm10", k=2, strand="+", format="txt", output="toString");

julia> print(res)
# [ GGGenome | 2018-07-01 22:59:01 ]
# database:     Mouse genome, GRCm38/mm10 (Dec, 2011)
# query:        TTCATTGACAACATTGCGT
# count:        41
# name  strand  start   end     snippet snippet_pos     snippet_end
chr1    +       19461997        19462014        AGTTATTCAGCTTTCTATCACGATCAGAGAACAAGCTGAGAAAAGGATGTTTTTGCTTTTGCTTTTGTTTTTCTTCTTATTTTGGAGTTCTCATCCATGATTCATTGACACCATTGCTTTGGCCTCTGGGAAGGGCAGCATATCTGGGTAAAAGCAGATAGCAGAGCAAATCTGCTTACTGCAACCAGCCAGGAAGGAAGCAATGAAAGCACGTTCAC  19461897        19462114
chr1    +       98281503        98281520        TCTAGTGAGGAGAAATGTAAGCTAACGTGATAAACATTGTTTCTGATACACTAATTAAACTGACTTTTGAAAAGATGGCTTACATGTCTATCTAACATGTTTCATTGACACCATTGCTATAGTATGTAATTTTAATGTAAAATAGCCTTCTTTGCAGGGAATCCAGCCTGCTGCTGAATCTTTAAATTTTCAGTGTCTGTTGTCATAGTAACCAGAAT  98281403        98281620
...

Understanding output parameters

By default, gggsearch() returns a HTTP.Messages.Response object.

julia> query = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA";

julia> res = gggsearch(query, db="refseq", format="txt");

julia> typeof(res)
HTTP.Messages.Response

By setting output="toString", gggsearch() returns a String object.

julia> query = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA";

julia> res = gggsearch(query, db="refseq", format="txt", output="toString");

julia> typeof(res)
String

julia> println(res)
# [ GGGenome | 2018-07-01 22:25:16 ]
# database:     RefSeq complete RNA release 88 (May, 2018)
# query:        GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA
# count:        15
# query:        TCCCGCCGGCTTCTCCGGGATCGGTCGCGTTACCGCAC
# count:        10
# name  strand  start   end     snippet snippet_pos     snippet_end
NR_003279.1 Mus musculus 28S ribosomal RNA (Rn28s1), ribosomal RNA      +       2326    2363    GAAGGGACGGGCGATGGCCTCCGTTGCCCTCGGCCGATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCCAGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGGCCTCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCC      2226    2463
NR_003287.4 Homo sapiens RNA, 28S ribosomal N5 (RNA28SN5), ribosomal RNA        +       2574    2611    GGGACGGGCGATGGCCTCCGTTGCCCTCGGCCGATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCGTCCAGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCCG      2474    2711
...

By setting output="extractTopHit", gggsearch() returns a String object containing the top hit (Currently, only works with format="txt").

julia> query = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA";

julia> res = gggsearch(query, db="refseq", format="txt", output="extractTopHit");

julia> typeof(res)
String

julia> println(res)
NR_003279.1 Mus musculus 28S ribosomal RNA (Rn28s1), ribosomal RNA      +       2326    2363    GAAGGGACGGGCGATGGCCTCCGTTGCCCTCGGCCGATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCCAGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGGCCTCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCC      2226    2463