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Ancestral sequence reconstruction steps !
Last updated 2849 days ago by Surabhi Chaudhary Comments (1)
Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an...
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Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2851 days ago by Jit
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw...
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Convert VCF to tab-deilimited table
Last updated 2852 days ago by Seema Singh
Performed with GATK : java -Xmx8g -jar GenomeAnalysisTK.jar \ -T VariantsToTable \ -R reference.fa \ -V reference_genomes_GT.vcf \ -F CHROM -F POS -F REF -F ALT -GF GT \ -o reference_genomes_GT.table multiple_sample.vcf should also be...
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Learning Python Programming - a bioinformatician perspective !
Last updated 2852 days ago by Rahul Nayak Comments (1)
Python Programming is a general purpose programming language that is open source, flexible, powerful and easy to use. One of the most important features of python is its rich set of utilities and libraries for data processing and analytics...
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Creating conda environment for python2.7
Last updated 2859 days ago by Jit
TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on specifying a different path. Use the Terminal or an Anaconda Prompt for the...
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Installing python-numpy !
Last updated 2860 days ago by Jit
$ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose[sudo] password for urbe: Reading package lists... DoneBuilding dependency tree Reading state information... DoneThe...
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Tools for Protein-Protein Docking !
Last updated 2872 days ago by Poonam Mahapatra
Predicting the structure of protein–protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes....
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Ligand Docking Tools and Software !
Last updated 2872 days ago by Poonam Mahapatra
Ligand docking referred to cases where small molecule (“ligand”) is being docked into much larger macromolecule ("target"). The following is partial list of docking software, focusing on free (at least for academic institutes) and/or...
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Protein-Protein Interaction Sites Predictions !
Last updated 2872 days ago by Poonam Mahapatra
The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues...
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Binding Site Prediction in Protein !
Last updated 2872 days ago by Poonam Mahapatra
The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the...