findpos: 'Find SNP Position'

In yangjl/findpos:

Description

Find the physical position of a short sequence in a given genome.

Usage

findpos(blastbin = NULL, db, fa, iden, len)

Arguments

blastbin	The path of binary code for NCBI BLAST program. [String, default=NULL]
db	Path of database to BLAST against. [String]
fa	A fasta file of the sequences of interest. [String]
iden	Percent identity of the alignment. [interger, default=95]
len	Minimum length of the alignment. [interger, default=100]

Value

return a data.frame.

Examples

library("Biostrings")
library("findpos")
### Find the help document for the function
?findpos
### run
 res <- findpos(blastbin = "~/bin/ncbi-blast-2.4.0+/bin",
                db="example/16SMicrobialDB/16SMicrobial",
                fa="example/rna.fasta", iden=95, len=100)

yangjl/findpos documentation built on May 4, 2019, 2:28 p.m.