marufmd / irspot-sf

Prediction of Recombination Hotspots using Sequence Based Features

iRSpot-SF

Prediction of Recombination Hotspots using Sequence Based Features

Installation

No installation needed. Just download the files in a folder or download the iRSpot-SF-master.tar.gz file and extract it into your local directory. Following prerequisites are required to run the software.

1. Install python 3.4 or latest version
2. Install following python packages:
   • numpy
   • pandas
   • sklearn

Run the software:

Step 1: Go to the folder "input". Open the text file "input.txt". Enter the DNA query sequence in FASTA format.

Example of a DNA sequence in FASTA format:

>YDL087C 1.67     
ATGTCAACTATGTCAACGCCTGCCGCAGAACAACGCAAACTCGTCGAACAGCTGATGGGCAGGAC 
TTCAGTTTCCGCCACAACAGGTATTCGCATCAAAAAAGAGACCTCGGACTACACGATCCAAGATC 
TGCAAGTCATACCTTGTTGGCGAGTGCCCCTACGACCTGTTTCAGGGCACCAACAGAGCCTGGGA 
AAATGCCCGCAGATGCATCTTACCAAGCATAAAATTCAGTACGAGAGAGGGTCAAGCAGGGCAAA 
ACGTTTCCCGAATTCGAAAGAGAATATCTGGCCATTCTATCTCGGTTGTTAATGAGTGTAATGGC 
CAGATATCCGTAGCACTACAAAATCTAAAACACACCGCTGAGAACGAATGAAGATTCAGCAGGTT 
ACCGAAGAACTAGATGTCTTGGACGTGCGGATAGGCCAATGGGACAAGAGATTGATTCTTTAATT 
CGTGCAGATGAAGTCAGTATGGGTATGCTACAGCAGTCAAATTACAAGAACTGATTAGTAAAAGG 
AAAGAAGTTGCAAAACGTGTACGAAACATACAGAAAACGTGGGCCAGAGCGCCCAGCAAAAGTTA 
CAGGTTTGCGAGGTGTGTGGGGCATCCTATCGCGTTTAGATACAGACAGAAGGCTTGCTGACCAC 
TTCTTGGGGAAGATTCATCTGGATATGTCAAGATGAGAGAGGATTATGATCGGCTAATGAAGAAT 
AACCGGACAACTAACGCAGCAAGACAGCTACTACACTACCCGGAAGACGCTTTGTGTA

Step 2: Type the following command in the terminal:

$ python  model.py

Step 3: Go to the folder "output". Open the text file "output.txt". It will show you the prediction for the DNA query sequence of "input.txt". HOT is shown for HOTSPOT and COLD for COLDSPOT. For the sample DNA sequence it'll show:

HOT

N.B., If the DNA sequence is not in FASTA format, it will not predict anything.