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Sequence search against a set of local sequences (local database) using phmmer

in Proteomics/Sequence Analysis/Softwares by

PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version 3.1 b2). It is available online as a web server and as well as a part of the HMMER stand-alone package (http://hmmer.org; version 3.1 b2). HMMER offers various useful features such as multiple sequence alignment including the file format conversion.  Continue reading “Sequence search against a set of local sequences (local database) using phmmer” »

Vina output analysis using Discovery Studio visualizer

in Docking/Drug Discovery/Softwares by

The discovery studio (DS) visualizer [1] offers several features for analyzing docking results. In previous articles (“Tutorial: Vina Output Analysis Using PyMol” and “Video Tutorial: Autodock Vina Result Analysis with PyMol“), the analysis of Autodock Vina [2] result using the Pymol viewer [3] was explained. In this article, the Autodock Vina result is being analyzed in the DS visualizer [1]. Continue reading “Vina output analysis using Discovery Studio visualizer” »

Installing and executing ProtTest3 on Ubuntu

in Phylogenetics/Softwares/Tools by

Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criterions: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. Continue reading “Installing and executing ProtTest3 on Ubuntu” »

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