genomeSearch: Get genome sequence from GGGenome

In dritoshi/genesearchr: Fast full-text and DNA search in NCBI RefSeq, UniProt-KB and genome sequence

Description

This function queries DNA sequence from GGGenome.

Usage

  genomeSearch(query, db, k)

Arguments

query	DNA sequence (character)
db	genome name (character) hg19, mm10, rn5, galGal4, xenTro3, danRer7, ci2, dm3, ce10, TAIR10, rice, bmor1, refseq, ddbj
k	Maximum number of mismatches/gaps. (default: 0) (numeric vecter)

Details

Search operators: See http://gggenome.dbcls.jp/en/help.html

Species:

• Human: "hs19"

• Mouse: "mm10"

• Rat: "rn5"

• Chicken: "galGal4"

• Frog: "xenTro3"

• Zebrafish: "danRer7"

• Sea squirt: "ci2"

• Fly: "dm3"

• Worm: "ce10"

• Arabidopsis: "TAIR10"

• Rice: "rice"

• RefSeq: "refseq"

• DDBJ: "ddbj"

Value

A GRanges Object

Examples

my.mm10.dna <- genomeSearch(query = "TTCATTGACAACATTGCGT", db = "mm10", k = 2)

dritoshi/genesearchr documentation built on May 15, 2019, 2:12 p.m.