PLEK2: a novel method for predicting lncRNA and mRNA based on sequence intrinsic features and Coding-Net model (Upgraded version of PLEK) =========================================================== PLEK: predictor of long non-coding RNAs and mRNAs based on k-mer scheme (PLEK download | SourceForge.net) =========================================================== INSTALLATION ------------- LncRNA participates in many important regulatory activities of organisms. Its biological structure is similar to messenger RNA (mRNA), in order to distinguish between lncRNA and mRNA (messenger RNA) transcripts more quickly and accurately, we upgraded the alignment-free PLEK to PLEK2. Requirements ------------ + [Linux] + [Python version > = 3.8.5] (http://www.python.org/) install regex package $ pip install regex install keras==2.4.3 package $ pip install keras==2.4.3 install pandas package $ pip install pandas install tensorflow==2.4.1 package $ pip install tensorflow==2.4.1 install bio version >= 1.3.2 package $ pip install bio install numpy package $ pip install numpy==1.19.2 -------------------------------------------------- Steps: 1. Download PLEK2_model_v3.tar.gz from https://sourceforge.net/projects/plek2/files/ and decompress it. $ tar zvxf PLEK2_model_v3 2. Compile PLEK2_model_v3 $ cd PLEK2_model_v3 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) #-fasta The name of a fasta file, its sequences are to be predicted. Examples: $ python PLEK2.py -i PLEK2_test.fa -m ve ============== Haotian Zhou, Master School of Computer Science and Engineering, Xi'an University of Technology, 5 South Jinhua Road, Xi'an, Shaanxi 710048, P.R China Aimin Li, PhD School of Computer Science and Engineering, Xi'an University of Technology, 5 South Jinhua Road, Xi'an, Shaanxi 710048, P.R China 2350837044@qq.com liaiminmail AT gmail.com emanlee815 AT 163.com