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Project Description

UPDATE LOGS:
#===========
# 2014-06-26
#===========
svm_grid_modelling_singlet.py was updated. This script is related to PLEK_howto_generate_scripts.doc and PLEK_generate_scripts.R, and is called by PLEKModelling.py.


INSTALLATION
Pre-requisite:
1. Linux
2. C/C++ compiler (i.e. gcc, g++)
3. Python 2.5.0 or later versions (http://www.python.org/)

Steps:
1. Download PLEK.1.2.tar.gz from https://sourceforge.net/projects/plek/files/
and decompress it.
$ tar zvxf PLEK.1.2.tar.gz
2. Compile PLEK.
$ cd PLEK.1.2
$ python PLEK_setup.py


USAGE
python PLEK.py -fasta fasta_file -out output_file -thread number_of_threads
-minlength min_length_of_sequence -isoutmsg 0_or_1 -isrmtempfile 0_or_1

Examples:
1. $ python PLEK.py -fasta PLEK_test.fa -out predicted -thread 10
2. $ python PLEK.py -fasta PLEK_test.fa -out predicted -thread 10 -minlength 150

System Requirements

System requirement is not defined

Download Package list

Latest 5 files
Name Size Date Download count
paper_mirPD_A_pattern.pdf 1.5 MB 2019-03-10 13:05 0
paper_Prediction_of__Cancer.pdf 695.6 KB 2019-03-10 13:05 0
paper_PigVar_a_database.pdf 1.4 MB 2019-03-10 13:04 0
paper_PLEK_a_tool.pdf 354.3 KB 2019-03-10 13:04 0
paper_Network_based_identification.pdf 2.1 MB 2019-03-10 13:04 0
All Files
pub
paper_mirPD_A_pattern.pdf1.5 MB2019-03-10 13:050
paper_Prediction_of__Cancer.pdf695.6 KB2019-03-10 13:050
paper_PigVar_a_database.pdf1.4 MB2019-03-10 13:040
paper_PLEK_a_tool.pdf354.3 KB2019-03-10 13:040
paper_Network_based_identification.pdf2.1 MB2019-03-10 13:040
paper_Genome_wide_discovery.pdf2.6 MB2019-03-10 13:040
paper_Genome_wide_analyses.pdf1.5 MB2019-03-10 13:030
paper_Genome_scale_identification.pdf1.2 MB2019-03-10 13:030
paper_Genome_Wide_Identification.pdf994.1 KB2019-03-10 13:030
paper_Diversified_Control_Paths.PDF2.1 MB2019-03-10 13:030
paper_Detection_of_Piwi.pdf3.7 MB2019-03-10 13:020
paper_Detecting_pan_cancer.pdf3.7 MB2019-03-10 13:020
paper_DNA_methylation_signatures.pdf942.0 KB2019-03-10 13:010
paper_ALDB_A_Domestic.pdf820.6 KB2019-03-10 13:010
PLEK.1.2.readme.txt9.2 KB2016-01-12 22:465
PLEK.1.2.tar.gz55.2 MB2016-01-12 22:436
data_vertebrate
zebrafish.rna.fna.20130813.fa.1row.200_filt530.9 MB2015-03-06 23:4412
frog.rna.fna.refseq.20130909.fa.1row.200_filt520.9 MB2015-03-06 23:444
cow.rna.fna.refseq.20130911.fa.1row.200_filt530.9 MB2015-03-06 23:446
Xenopus_tropicalis.JGI_4.2.72.ncrna.fa.1row.200_filt495.9 KB2015-03-06 23:446
Sus_scrofa_refseq_20130925_fa.1row.200_filt57.5 MB2015-03-06 23:445
Sus_scrofa.Sscrofa10.2.72.ncrna.fa.1row.200_filt4126.2 KB2015-03-06 23:446
Pongo_abelii_refseq_20130925_fa.1row.200_filt59.8 MB2015-03-06 23:443
Pongo_abelii.PPYG2.72.ncrna.fa.1row.200_filt4168.4 KB2015-03-06 23:444
Pan_troglodytes_refseq_20130925_mRNA.200_filt43.8 MB2015-03-06 23:443
Pan_troglodytes.CHIMP2.1.4.72.ncrna.fa.1row.200_filt4505.6 KB2015-03-06 23:443
Macaca_mulatta_refseq_20130925_fa.1row.200_filt512.0 MB2015-03-06 23:443
Macaca_mulatta.MMUL_1.72.ncrna.fa.1row.200_filt4155.4 KB2015-03-06 23:443
Gorilla_gorilla_refseq_20130925_fa.1row.200_filt593.8 MB2015-03-06 23:443
Gorilla_gorilla.gorGor3.1.72.ncrna.fa.1row.200_filt4159.3 KB2015-03-06 23:434
Danio_rerio.Zv9.72.ncrna.fa.1row.200_filt4302.6 KB2015-03-06 23:435
Bos_taurus.UMD3.1.72.ncrna.fa.1row.200_filt479.4 KB2015-03-06 23:435
data_mouse
gencode.vM2.lncRNA_transcripts.fa.60158.2 MB2015-03-06 23:427
mouse_refseq_mRNA_6015.fa18.2 MB2015-03-06 23:426
data_human
human_rna_fna_refseq_mRNA_2238975.6 MB2015-03-06 23:417
human_gencode_v17_lncRNA_2238923.6 MB2015-03-06 23:413
human.rna.fna.refseq.mRNA.34571116.9 MB2015-03-06 23:4016
tutorial
PLEK.1.2.readme.txt9.1 KB2014-06-27 00:107
PLEK_howto_generate_scripts.doc27.0 KB2014-06-24 15:164
howtobuildmodel1.2_step4_use.mp47.0 MB2014-06-24 14:552
howtobuildmodel1.2_step3_build.mp472.8 MB2014-06-24 14:555
howtobuildmodel1.2_step2_configure.mp432.8 MB2014-06-24 14:544
howtobuildmodel1.2_step1_preprocess.mp412.6 MB2014-06-24 14:548
how_to_use_PLEK.1.2.mp420.6 MB2014-06-24 14:543
how_to_install_PLEK.1.2.mp413.6 MB2014-06-24 14:546
how_to_build_model.1.2.mp423.9 MB2014-06-24 14:543
PLEK_1.0_howto_install_and_use.mp46.8 MB2014-03-22 14:564
PLEK_1.1_howto_install_and_use.mp439.0 MB2014-03-22 14:525
other
maize_ens_linli.range24.1 KB2014-06-24 15:054
maize_ens_linli.model188.7 MB2014-06-24 15:052
PLEK.1.1.tar.gz53.5 MB2014-03-29 11:183
PLEK.1.1.readme.txt4.2 KB2014-03-29 11:131
PLEK.1.0.readme.txt4.0 KB2014-03-21 14:471
PLEK.1.0.part1.tar.gz17.6 MB2014-03-21 14:134
PLEK.1.0.part2.tar.gz17.4 MB2013-11-16 17:267
PLEK.1.0.part3.tar.gz18.5 MB2013-11-16 17:251