How to install Perl modules manually, using CPAN command, and other quick ways
...e are now dependent all these tiny magicians :). # yum install perl-CPANOutput of yum install perl-CPAN comm...BioPerl in your server/computer. # sudo apt-cache search perl BioPerl Output will be like as follows: bio...3949 days ago
Five unique traits of effective computational biologist
...o my supervisor most of the computational biologist, don't know what they are doing biologically. Even they struggle to explain their own programs output and results. Therefore, It is...3949 days ago
Public Databases for Bioinformatics !
...o = multiprocessing.Queue() for i in xrange(NSIMS): todo.put(i) for i in xrange(NPROC): todo.put('FINISHED') ofp = ProcessSafeOPStream( open("output.txt", "w") ) pids = [] fo...1138 days ago
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Check the Size of a directory & Free disk space.
...s in kilobytes (default). The last line of the output gives you the total size of t...dquo;command with some flag gives you a better output than the default one. The opt...ives you a grand total as the last line of the output. So if your directory occupie...3701 days ago
A guide for complete R beginners :- Getting data into R
...s in an object at any time by typing its name; x will produce the output ‘[1] 1 2 3 4 5′...ount of Something”) Note Nothing will appear on screen, the output is going to the file Also it...3356 days ago
Most Commonly used Awk by Bioinformatician
...where column 3 is larger than column 5: awk '$3>$5' input.txt > output.txt extract column 2,4,5: awk '{print $2,$4,$5}' input.txt > output.txt awk 'BEGIN{OFS="\t"}{pri...3911 days ago
List of In-silico Binding Site Prediction Tools
...protein-binding sites defined by interactions with small molecules. The output is a detailed list of the sha...e input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the sha...3743 days ago
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Research fellow (PhD candidate) in computational biology – 2 positions
...ll analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will...3661 days ago
Post-Doc Positions at the Institute of Evolution, University of Haifa, Haifa, Israel
...y, for Post-Docs experts in bioinformatics with a background of good understanding biological questions. That is that can independently handle raw output data of RNA-seq / miR seq/ Ge...3530 days ago
Bioinformatics 101 - Running BLAST
How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered live at the Tomato Disease Worksho...3896 days ago
R script to visualize fastANI core-genome comparison
...ose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR packa...visual_file=commandArgs(TRUE)[3] library(genoPlotR) #Read fastANI output comparison...1100 days ago
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Tryst with a Bioinformatician # Dr Altan Kara
...run by only looking at the results instead of just blindly trusting the output of the bioinformatics tools....nmental control. In other words, one should always easily control input output directories, modify files or...2361 days ago
collinearity: scripts to parse and analyse MCScanX collinearity output
scripts to parse and analyse MCScanX collinearity outputTags: collinearity, scripts, parse, analyse, MCScanX, collinearity, output
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“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve correspond...Tags: perl, tool, conveniently, parse, RepeatMasker, output, files
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Comment on "Benchmarking Perl Module !"
...k for 100 iterations: timethese(100, { 'MyModule' => \&benchmark_my_module, }); Analyze the results: The timethese function will output the results of the benchmark,...414 days ago
Comment on "Short-read assembly using Spades !"
...ce. The command for running SPAdes is usually as follows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq Here, "output_directory" is the name of the...414 days ago