Prediction of Recombination Hotspots using Sequence Based Features
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.
- Install python 3.4 or latest version
- Install following python packages:
- numpy
- pandas
- sklearn
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.