How to install Perl modules manually, using CPAN command, and other quick ways
As a bioinformatics programmer, and crunchy data analyser you need to insta...odules using CPAN, make sure the cpan command is working. Following are the...e is not installed.# cpan-bash: cpan: command not found# perl -MCPAN -e she...Parameters for the 'perl Makefile.PL' comma...3944 days ago
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Taverna Workflow Management System
Taverna is an open source domain independent Workflow Management System – a suite of tools used to design and...r (which allows remote execution of workflows). Taverna is also available as a Comma...3910 days ago
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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.pl3862 days ago
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Bio++ : C Language libraries for your biological need
C has always been a language that never attempts to tie a programmer down - it allows for easy implementation, it co...switch between upper/lower case, etc.Applications: read options from a file or comma...3942 days ago
BioRuby :Ruby packages for biologist
BioRuby is a package of Open Source Ruby code, with classes for DNA and protein...and is still in progress. Currently, there are over 80 files and 15,000 lines (except comment-only lines) in our source code. This mig...3941 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next generation quantitative genetics in plants. Jiménez-...cs 11(Suppl 12):S1, 2010 Full Text Links to Linux command-line tutorials and resources...rial Greg Goebel's awk tutorial Executing an awk comma...3773 days ago
List of In-silico Binding Site Prediction Tools
Following are the list of In-silico Binding Site Prediction in Proteins tools CASTp : http://sts.bioengr.uic.edu/ca.... It was developed in the C programming language and is currently available as comma...3738 days ago
RNA-Seq Data Pathway and Gene-set Analysis Workflows
It describe the GAGE (Luo et al., 2009) /Pahview (Luo and Brouwer, 2013) workflows on&...nting, data preprocessing, gene set test, to pathway visualization in about 40 lines of codes. The same workflow c...3827 days ago
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Bioinformatics @ TATA MEMORIAL CENTRE, NAVI MUMBAI
TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER...e kinase shRNA libraries in head and neck squamous call carcinoma (HNSCC) cell lines DBT A/C No. 3071, Dr. Amit D...3836 days ago
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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 l...3891 days ago
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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 -que...1095 days ago
Comment on "Sibelia: A comparative genomics tool"
...n "Directory for temporary files"). Above commands will run "Sibelia" on the fi...ermutations of the synteny block. It has two lines for each input sequence: 1....ijn grahp for k=25, one can use the following command line: Sibelia -k run.st...1279 days ago
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