How to install Perl modules manually, using CPAN command, and other quick ways
...l Perl modules using CPAN, make sure the cpan command is working. Following are the...AN module is not installed.# cpan-bash: cpan: command not found# perl -MCPAN -e she...)? [ask]Parameters for the 'perl Makefile.PL' command? []Parameters for the 'perl B...3950 days ago
3940 days ago
Taverna Workflow Management System
...rna Workbench(the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick executi...3916 days ago
3653 days ago
Detect the sequence pattern and its location in fasta file with match and mismatches information.
This script is one of my old script to detect some centromeric pattern in chromosomes. User can also control the number of mismatches allowed through command line .. To run: perl centro.pl3868 days ago
3866 days ago
Bio++ : C Language libraries for your biological need
...rt text to any other type and vice versa, remove spaces, tokenize, switch between upper/lower case, etc.Applications: read options from a file or command lineetc. Some of the librari...3948 days ago
3702 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...or, BMC Bioinformatics 11(Suppl 12):S1, 2010 Full Text Links to Linux command-line tutorials and resources...e Barnett's awk tutorial Greg Goebel's awk tutorial Executing an awk command from R to simplify data explo...3780 days ago
List of In-silico Binding Site Prediction Tools
...n pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program. A GUI is...3744 days ago
Linux operating system aimed at scientists
...Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just...3394 days ago
3305 days ago
Internship in Computational Biology
...rmal applications are due by Sunday 2nd December 2012. Requirements: This position requires a good understanding of genetic problems, a good command of at least one scripting lan...3531 days ago
JRF Bioinformatics at National Institute of High Security Animal Diseases (ICAR)
...ipline). Desirable : Exposure of working in research environment, Good command over written/spoken English a...ed areas. Desirable: Exposure of working in research environment, Good command over written/type written/spo...3296 days ago
3181 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 t...3897 days ago
3520 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003...1102 days ago
R script to visualize fastANI core-genome comparison
...e comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse command line arguments query_fasta=commandArgs(TRUE)[1] subject_fasta=c...1102 days ago
Monitor running jobs on Linux server
You as a bioinformatican run lots of program on your servers. Sometime the shared server is also used by your colleague. If server is busy you sometime need to check the running programs and want to monitor the running programs as well. The "top" command will come in handy when you need to find o...Tags: Bioinformatics, Computational Biology, Linux, Command, Top, Running, Processes, Server, Monitor
3621 days ago
Tags: Bioinformatics, Computational Biology, Linux, History, Search, Find, Delete, Shell, Command
3615 days ago
Comment on "Benchmarking Perl Module !"
...hmark module: Install the Benchmark module: If you don't already have the Benchmark module installed, you can install it using the following command: cpan Benchmark Write b...416 days ago
Comment on "Short-read assembly using Spades !"
...ic or FastQC. Running SPAdes: After quality control, the next step is to run SPAdes. This can be done through a command-line interface or a graphical user interface. The command for running SPAdes is usually...416 days ago