scipion-chem-blast

BLAST is the well known program for finding regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. In this plugin we incorporate functionalities both for local and web-server BLAST.

Installation

A) Requirements

In order to use this plugin, you need to install first scipion-chem.

B) Installation steps

• Install the stable version

  Through the plugin manager GUI by launching Scipion and following Others >> Plugin Manager, or

scipion3 installp -p scipion-chem-blast

• Developer’s version

  1. Download repository:

  git clone https://github.com/scipion-chem/scipion-chem-blast.git

  2. Install:

  scipion3 installp -p /path/to/scipion-chem-blast --devel

Warning

Installation of the stable version through the Plugin Manager or with the command provided above is not available yet.

Please install the developer version until a stable version is released, or install the latest stable version with the following steps:

cd /path/to/scipion-chem-blast && git checkout master && scipion3 installp -p . --devel

Protocols

• Blast NCBI download: Predicts the pockets of an atomic structure based on its concavities (using alpha-speheres) and its electrostatics.

• Create local database: Predicts the pockets of an atomic structure based on its concavities (using alpha-speheres) and its electrostatics.

• BLAST search: Predicts the pockets of an atomic structure based on its concavities (using alpha-speheres) and its electrostatics.