#BLAST 2 SEQUENCES HOW TO#
#BLAST 2 SEQUENCES INSTALL#
#BLAST 2 SEQUENCES ZIP FILE#
#BLAST 2 SEQUENCES MANUAL#

We will perform a default BLASTp search on these to find out what proteins they are. Save this page as proteins.fasta and put in the same directory as the pdbaa folder we downloaded earlier. You can get download sample protein sequences for this tutorial here.

We will now search a few protein sequences against the database and retrieve the results. You can find an extensive overview of these here. Ensure you know which search strategy is appropriate for your data and database type. This includes blastn, blastp, blastx, tblastn and tblastx. Exercise 2: performing a basic BLASTp searchīLAST+ search strategies are run by typing the type you want on the command line followed by the input options.

#BLAST 2 SEQUENCES HOW TO#

We will see later how to create this database ourselves. This denotes that a protein database has been created. You will notice each has a ‘p’ after the period. Each of these allows for a different type of search to be performed. Inside there is a folder called pdbaa which contains many files, all of which begin with ‘pdbaa’.

#BLAST 2 SEQUENCES ZIP FILE#

We will use a subsection of this database for this tutorial.ĭownload the zip file here. This is a dataset containing all the protein sequences associated with PDB files (protein structure files). These are often very large and are split into several files (take a look at the amount of files needed for nr). Several pre-made databases are provided by NCBI here. Most often when using BLAST+ we wish to ether create a custom database or a local version of a pre-made database to BLAST against. If you get an output like “BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified” then BLAST+ is installed correctly No matter what approach you used for installation, test that this works by typing Make sure you change this to whatever path you set for the installed files. This tells the operating system to add the directory containing the BLAST programs to our path. For Linux, open a new terminal and type the following commands:Įcho PATH=$PATH:~/tools/ncbi-blast-2.10.1+/bin ».bashrc As stated, with conda, Windows or OSX installations this should be done automatically by the installation process. The path tells the computer the location of each program so that we do not have to type out the location each time. To run the programs from the command line we need to place them in our Path. For this example, we will say the path (found with pwd) is ~/tools/ncbi-blast-2.10.1+/ You should now have a folder called ncbi-blast-2.10.1+ (or whatever version you downloaded). Once downloaded, extract to a tools folder inside your home directory. For example, for an Ubuntu installation we want the ncbi-blast-2.10.1+-圆 file. For Linux we need to do some extra steps. For OSX and Windows, follow the instructions on the downloaded exe or dmg and this should do the installation. If you wish to use the NCBI files, you can do the following:įirst go here and download the appropriate version. It will do all the installations automatically for you. I strongly suggest using conda for this, which you can get from here amd then get the BLAST package here.

#BLAST 2 SEQUENCES INSTALL#

In order to run BLAST+ we must download it, install it and set our Path to point to it. Exercise 1: BLAST+ installation and using a pre-formatted a database Here, only a subset of features and basic usage will be covered. This covers all of the functionality of BLAST+.

#BLAST 2 SEQUENCES MANUAL#

The user manual for BLAST+ is here and contains instructions on installation of the command line tools, although I recommend using conda for this as it is easier to keep updated. You can download it from here or install using conda. The command line (UNIX or Windows) version of BLAST is named BLAST+. We will cover basic BLAST searching, modifying parameters, modifying output files, creating your own database, online searching and hit sequence extraction. The objective of this lab is to get accustomed with performing BLAST searches from the command line (called BLAST+).

Blast 2 sequences