NUCPROFILER:

DNA shape profile for genomic fragments.

NUCPROFILER has two scripts.

• nucprofiler_intraparams.R calcuates intra base pair parameters like "ProT","Stretch","Buckle","Shear","Opening","Stagger" as well as Electrosatic potnetial (EP) and minor groove width (MGW).

• nucprofiler_interbaseparams.R calcuates intra base pair parameters like "HelT","Roll","Tilt","Shiftr","Slide", and "Rise".

Prerequisite R packages

library("seqinr")
library(stringi)
library(tools)
library(data.table)

Usage

user@machine:~nucprofiler$ Rscript nucprofiler_intraparams.R      example/small.fasta 
user@machine:~nucprofiler$ Rscript nucprofiler_interbaseparams.R  example/small.fasta

A sample Bash script (batch)

An bash script to run in batch is provied.

#!/bin/bash
for file in `cat list_of_fasta`
do
  
  Rscript nucprofiler_interbaseparams.R $file
  Rscript nucprofiler_intraparams.R     $file
  
done

Query table information

The query table is inside data folder.

References

• J. Li et al. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic Acids Res. 45, 12877-12887 (2017)

• T.P. Chiu et al. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.Nucleic Acids Res. 45, 12565-12576 (2017)

Example

The example folder has there types of files representative of small, medium and big fasta files.

Sample R Markdown documents

For nucprofiler_intraparams.R the R makrdown is provided.

New in the latest version

Version: 1.0.1 Date: 2018-06-01

• fixed some typos and paths
• added query table publication
• added example fasta files

Outlook

1. Add Matrix plotting option.
2. Add dinucleotide based porperty.