PLEKv2

PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the Coding-Net model

INSTALLATION
-------------
We upgraded PLEK to PLEKv2. All you need is RNA sequences (fasta file).

Steps:
1. Download PLEK.2.1.tar.gz from * and decompress it.
$ tar zvxf PLEK.2.1.tar.gz
2. Compile PLEK2.1
$ cd PLEK2.1
3. decompress Coding_Net_kmer6_orf.h5.bz2 model
$ bunzip2 Coding_Net_kmer6_orf.h5.bz2
4. decompress Coding_Net_kmer6_orf_Arabidopsis.h5.bz2 model
$ bunzip2 Coding_Net_kmer6_orf_Arabidopsis.h5.bz2

USAGE
Python PLEK2.py -i fasta_file -m model(ve: vertebrate , pl: plant)

Examples:
$ python PLEK2.py -i test.fasta -m ve

Aimin Li, Haotian Zhou, Siqi Xiong, Junhuai Li, Saurav Mallik, Rong Fei, Yajun Liu, Hongfang Zhou, Xiaofan Wang, Xinhong Hei, Lei Wang. PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model. BMC Genomics 2024, 25(1):756. https://doi.org/10.1186/s12864-024-10662-y

Features

predicting lncRNAs
identifying lncRNAs
distinguishing lncRNAs

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Additional Project Details

Registered

2022-08-02

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