First of all, find the lastest verion of BLAST
from following ftp.
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Download the appropriate version for your system. And then install it following here.
### biostrings
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
### install devtools
install.packages("devtools")
### install packages in development
devtools::install_github("yangjl/findpos")
The usage information can be found by typing ?findpos
, which is the major function for this task.
To run it, first of all, set up a blast
database, i.e. example/16SMicrobialDB/16SMicrobial
. And then specify the code for BLAST
program, i.e. ~/bin/ncbi-blast-2.4.0+/bin
. Note, the sequences of interest should be fasta
format, i.e. example/rna.fasta
. Finally, specify your mapping parameters, such as percent identity (iden
) and mapped seq length (len
). And then you just click and run.
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)