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Awesome Open Source

ViroBLAST Standalone Web Server

Introduction

This standalone ViroBLAST server suite of programs was designed to be similar to the NCBI BLAST server and command-line NCBI C++ Toolkit BLAST applications referred as the BLAST+ applications. It incorporates most features that exist in NCBI BLAST+ program, and adds new features to extend the utility of BLAST. It was created to facilitate verification of the origins of Human Immunodeficiency Virus (HIV) sequences derived from various experiments, and then was developed into the standalone web server for maximum utility in other research fields. It is recommended that users have experience in installation and running standalone NCBI BLAST+ programs when installing, configuring and customizing ViroBLAST. After files are uncompressed, ViroBLAST server is ready to be used immediately. Users then can configure and customize sequence databases to manage their own BLAST web server tailored to meet their specific research purpose.

Features

  • Customize public and user's local sequence databases.
  • Blast against user's sequence data set by uploading sequence file in FASTA format.
  • Blast against multiple sequence databases selected by user.
  • Summarize the BLAST output and easily navigate the result.
  • Download sequences in database that match user's query sequence.

Installation of the standalone ViroBLAST server

After downloading the file viroblast.tar.gz, place it into document directory of HTTPD server in your computer and uncompress it by

gzip -d viroblast.tar.gz
tar -xvpf viroblast.tar

It is important to have the parameter "p" in tar options. It will preserve file access options stored in the distribution. Directory for the BLAST output (data) should have readable, writeable and executable permissions for everyone (777).

After you have uncompressed the distribution file, the directory "viroblast" will be created. You can access the ViroBLAST home page via URL:

http://your_hostname/viroblast/viroblast.php

Configuration of BLAST program

The standalone ViroBLAST server runs the NCBI BLAST+ program and has been tested on Linux, Mac OS X and Sun OS. The distribution comes with a standalone BLAST+ program for linux/x64. It is your responsibility to download appropriate standalone BLAST+ for your computer's operating system from NCBI ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/). After you have downloaded the standalone BLAST+, uncompress it and put in a directory you want, then, change the path to "blast+" program into server configuration file (viroblast.ini).

Configuration and customization of BLAST sequence databases

This distribution comes with 2 BLAST databases to test. "Nucleotide test database" - sample nucleotide database and "Protein test database" - sample protein database. These databases are configured to be searchable immediately. After testing, you need to set up your sequence databases for the standalone ViroBLAST server. It is necessary to follow these steps:

  1. Put sequence FASTA file in appropriate directory under ./db/ (./db/nucleotide/ or ./db/protein/).
  2. Run "makeblastdb" program, available from the NCBI ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) to format the sequence database.
  3. Add name of the database into server configuration file (viroblast.ini). The format is: "database_file_name => database_name_for_display". If there are more than one database, put comma "," between them.

Directories and Files in the distribution

Root directory (./viroblast/):

  • viroblast.php: viroblast home page.
  • blastresult.php: blast result output page.
  • blast.pl: perl program executes blast+ program and formats the output.
  • sequence.php: page showing sequences ready for download.
  • download.php: download sequences.
  • viroblast.ini: Default configuration file for the ViroBLAST server.

./viroblast/blast+/

  • Default standalone BLAST+ program for linux/x64 downloaded from NCBI.

./viroblast/data/

  • Storage for BLAST output files.

./viroblast/docs/

  • Documents for the ViroBLAST server.

./viroblast/db/nucleotide/

  • Storage of nucleotide sequence databases for BLAST search.

./viroblast/db/protein/

  • Storage of protein sequence databases for BLAST search.

./viroblast/image/

  • Images used in ViroBLAST pages.

Server configuration file

This distribution comes with a default configuration file "viroblast.ini". The configuration file will set the path to blast+ program and what databases may be used with what programs.


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Database (92,849
Server (65,767
Perl (30,729
Protein (3,278