Part I : How to install NCBI BLAST on window 7
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hou to use and install ncbi blast offline cammandsActually every use of software includes three steps.
- Download
- Installation
- Uses
In this Part of tutorial, lets discuss two steps of the NCBI blast
process. blast+ is a new version of the blast package from the NCBI.
The blast+ package consists of a number of stand-alone programs, for searching sequence databases, creating blast databases and masking low complexity sequence.
Benefits of NCBI blast+ :
- Easy to local blast searhcers, and easy to run remote searches at the NCBI from the command line.
- You can save search strategies and run them again later.
- Flexible output of blast results. For example, you can get tab delimited output AND choose which columns of information are included.
- blastx efficiency has apparently been increased.
- An option to enable multiple threads to be run for local blast searches
- Blasting 2 sequences against each other is now easier
1. Download
- Latest executable of NCBI stand alone BLAST can be download from HERE. This directory contains executable for Window, Linux and Mac. Lets go with window executable. You can simply download it your favorite location (desktop, for me).
- Double click on downloaded files will resulted in a directory with the three files : Uninstaller, bin and doc folders. All executable will be in bin folder while all documentation will be in doc folders.
- Since all BLAST executable are non GUI therefore you have to access those executable through command line option of Window cmd.
2. Uses
bin folder of of NCBI local BLAST programms contains two type of program. remember that you can always use 'program name -help' command to know more about that program. For example, if you want to know abput blastp then use 'blastp -help'.
- .exe files
- PERL scripts
.exe files are three used for three different purpose
- database searching
- creating and working with database
- sequence masking utilities
Sequence Masking Utilities
| segmasker | used to mask repeats and low-complexity regions in a genome sequence |
| dustmasker | used to identifies and masks out low complexity parts of a genome using a new and improved DUST algorithm |
| windowmasker | used to identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. |
Database Searching Utilities
| blastn blastp blastx psiblast tblastn tblastx | Explained here |
| rpsblast+ | searches a query sequence against a database of profiles, or score matrices, prepared by copymat, producing BLAST-like output |
| rpstblastn | searches database of profiles using a translated nucleotide query against |
| deltablast | Explained here |
Sequence Masking Utilities
| makeblastdb | command-line tool for creating BLAST databases |
| makembindex | utility that can index a set of nucleotide sequences |
| blastdbcmd | command-line tool to examine the contents of BLAST databases |
| makeprofiledb | used to make search sets for RPS-BLAST, including the specialized data needed by DELTA-BLAST |
| blastdbcheck | performs tests on BLAST databases to check their integrity |
| blastdb_aliastool | Use to manage the collection of BLAST databases and facilitate BLAST searches. |
| blast_formatter | formats both local and remote BLAST results |
| convert2blastmask | extracts the lower-case masks from its FASTA input and converts them to a file format suitable for specifying masking information to makeblastdb |
PERL Script
| legacy_blast | Script to convert NCBI C toolkit command line program and arguments into NCBI C++ toolkit command line program and arguments for the BLAST suite of programs |
| update_blastdb | Script to download the pre-formatted BLAST databases from the NCBI ftp server. |
Further Uses
Part II : How to use NCBI local BLAST+
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