Blast installation ncbi

Type "makeblastdb -in testdb. Type "makeblastdb -help" for advanced options. These database files are assumed to be downloaded already.

All Rights Reserved. Begin a free trial by filling out this form. For the executable formats we provide installers as well as tarballs; the source code is only provided as a tarball. Please be sure to use the most recent available version; this will be indicated in the file name for instance, in the sections below, version 2. For users with administrator privileges and machines MacOSX version Double click the newly mounted ncbi-blast Note: one must have root privileges to run these commands.

Download the tarball, expand it, change directories to the newly created directory, and type the following commands:. The base command is:.

This configuration is through information stored in special user environment variables. For 2. Screen shots of these steps are shown, with the first two steps in Figure 4a , and the rest in Figure 4b. Clicking more Click the icon to launch it. Test the installation before using this installation for actual work. The test commands groups into three categories:. Technically, there are three components for a blast search, the input query , the target database, and the blast program.

The test session below includes a set of representative commands, each testing a specific aspect of this example installation. First section is on general checking and execution with marked command matching examples in Figure 6A.

Retrieve a sequence from this database for use as a test query E :. Run a nucleotide search using blastn and the test query sequence G :.

The following focuses on database manipulation and example session is in Figure 6b. The output of a work session focusing on database management and creation: The input commands are underlined with their function explained by inserted text.

Take advantage of the installed swissprot database to retrieve set of sequences from it and save them to a file L for use as example input. Turn recording back on. National Center for Biotechnology Information , U. Search term. Author Information Tao Tao , Ph. NCBI Bookshelf. Created: May 31, ; Last Update: August 31, The archives for Linux and Mac OSX are available as gzip-compressed tar files named using the following convention:.

Here, the. These archives and their target platforms are listed in the table below. View in own window. The installation process from the disk image. The example working session below demonstrates an ftp download process using an ftp client in a Linux environment. In Mac OSX, a similar command line interface is available through the Terminal utility, which is generally under the Utilities folder.

The source code archive, "ncbi-blast-. Questions and feedback on source code compilation should be addressed to:. To install, simply extract the downloaded package after placing it under a desired directory. This can be accomplished by a single tar command, or a combination of gunzip and tar commands. Successful execution of the above commands installs the package and generates a new ncbi-blast This new directory contains the bin and doc subdirectories, as well as a set of informational files.

The bin subdirectory contains the programs listed below. A better approach is to have the system automatically set these variables upon login, by modifying the.

Once they are set, the system knows where to call BLAST programs, and the invoked program will know where to look for the database files.

Type the command "blastn -help" without quotes should display the program parameters of blastn in the console as shown below.