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readme_v2.txt 2013-07-05 3.0 kB 11 weekly downloads
p-TAREF_cli_v2.tar.gz 2013-07-04 1.3 MB 11 weekly downloads
change_miRNAs_in_p_taref.pl 2013-07-03 1.8 kB 11 weekly downloads
readme.txt 2013-01-03 3.4 kB 11 weekly downloads
how_to_change_mirnas_in_p-TAREF.txt 2012-10-08 2.4 kB 11 weekly downloads
Expression.tar.gz 2012-02-23 30.6 MB 11 weekly downloads
dependencies.tar.gz 2012-01-24 24.9 MB 11 weekly downloads
########################### changes in V2.0 of p-TAREF ########################################## No need to add AT in front of the transcript sequecnes as it is done automatically by the script run.pl ################## END ################################### ########################### Change miRNAs in p-TAREF ########################################## Download the code "change_miRNAs_in_p_taref.pl" form the directory run the code as perl change_miRNAs_in_p_taref.pl miRNA_file_in_fasta_format This code will change the default miRNAs with the new miRNAs, for which targets can be identified. The default miRNAs list is given in file named "miRNA", you can check the list of miRNAs after and before running the perl code. It is advisable to run p-TAREF on small example file after running the code change_miRNAs_in_p_taref.pl to check the result. ################## END ################################### Vesrion 2 of p-TAREF is out please download it from here or from the scbb web page http://scbb.ihbt.res.in/new/p-taref/down.html p-TAREF: A fast and accurate tool to Refine plant microRNA Target Prediction please visit http://scbb.ihbt.res.in/ 1.System Requirement 2.Installation 3.Taref description 4.Performance 1.System requirement: Linux 64 bit O.S. with Qt 4 Major Linux distribution comes with Qt 4 as installed package if Qt 4 is not installed then follow this simple procedure Installing Qt 4: For Ubuntu type "sudo apt-get install libqt4-dev" on terminal without quotes For other Linux distribution type "yum install qt4 libqt4-*" on terminal as root Or download Qt framework from http://qt.nokia.com/downloads 2.Installing: Extract p-TAREF_linux.tar.gz migrate to folder p-Taref_linux and on terminal type qmake-qt4 and then make as root ( for ubuntu sudo ) a binary named Installer, double click on Installer and a GUI will appear, click on checkbox and then on install button this will install all the dependencies needed by p-Taref. After installing all the dependencies installer will ask you where to install p-Taref, Default installation is on /home/(username)/p-TAREF but you can change it to some other folder. To run p-TAREF, click on binary p-TAREF and a GUI will appear which executes the command for p-TAREF, If you want to run p-TAREF on command line type java -jar p-TAREF.jar <number of processors>. 3.p-Taref description: p-TAREF takes the sequences in fasta format you can submit multiple sequences. p-TAREF might take some time depending on your sequence file size. p-TAREF steps runs concurrently on multiple processors. 4.Performance p-TAREF perform better then any other software for plant miRNA prediction for details please visit "http://scbb.ihbt.res.in/p-taref/performance1.html" For any queries, please drop a mail to ravish9@gmail.com, ravish@ihbt.res.in or ashwanijha.bioinfo@gmail.com For query, bugs or information please contact ravish@ihbt.res.in or ashwanijha.bioinfo@gmail.com Thank you
Source: readme_v2.txt, updated 2013-07-05