wangdi2014 / findingori Goto Github PK

Ori and Ter prediction for prokaryotic circular chromosomes.

findingOri("accession",,) # NCBI accession number
findingOri(,"file path" ,) # Local fasta file path, UNIX standard
findingOri("accession","v") # verbose, with plots
findingOri(,"file path" ,"v") # verbose, with plots

• First release.

FindingOri consists of a set of R files, with a wrapper that calls R packages and other source files. To run it you need to first install Prodigal under bash [ Installing Prodigal]. Called R packages are: seqinr, ape, stringr and pracma. You can then install from source as follows:

$ source("wrapper.R")

• Predicts Ori and Ter of small circular chromosomes from FASTA DNA sequences.

• The user need to ensure that the target chromosome is the only sequence.

• Runs quickly: findingOri analyzes the E. coli K-12 genome in 60 seconds on a modern MacBook Pro.

• Runs unsupervised.

• Website

• Author: Torbjörn Larsson

GPL