In my previous post, I have discussed that how to download the NCBI BLAST on Window 7 and what is the uses of different software of NCBI local BLAST package. In this Bioinformatic tutorial, I will try to explain that how to use these packages. In NCBI BLAST+, beside the regular BLAST programs like blastn, blastp, there are other several programs for specific purposes.
Also Read Part I : How to install NCBI BLAST on window 7
3. Installation
Notwithstanding the nature of program, you have to always make a database then use the program. As I mentioned previously, your working directory will contain two folders - bin and doc. Folder bin will be your working directory. So open your command prompt and direct it to your working directory i.e. bin
Now, we have to prepare our database. In this example, my database contains nucleotide and stored in data.txt file while my query sequences are stored in query.txt.
NOTE: Please keep in mind that you can know all option for every BLAST programs by typing 'PROGRAM NAME -HELP'. For example, if you want to know the all option for 'blastn -HELP'
Since, I am using the nucleotide sequence then I will use blastn options. Lets create database for our database data.txt by typing these command in your command prompt. Depending upon size of yout
database, this process will take few seconds to several minutes. database formatting will results in three file - .nhr, .nin and .nsq file. Now when your database is ready for BLAST, you are ready for blast. You can simply go for blastn following this command
Hope this will help, if you have any problem, then do let me I will try to solve the issue.
Note to me : Use -outfmt 6 to get results in tabular form
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