November 2017
Intermediate to advanced
472 pages
11h 21m
English
book
Basic Applied Bioinformatics
by Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
Content preview from Basic Applied Bioinformatics
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.
CHAPTER 13Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)
CS Mukhopadhyay and RK Choudhary
School of Animal Biotechnology, GADVASU, Ludhiana
13.1 INTRODUCTION
BLASTp is a set of programs that searches the protein databases using an amino acid sequence as the query. There are four different algorithms, with well‐defined applications in BLASTp: blastp, psi‐blast, phi‐blast and delta‐blast.
13.2 OBJECTIVE
To search a homologous protein sequence from the protein database, using the given amino acid sequence as query.
13.3 PROCEDURE
13.3.1 Protein‐protein BLAST (BLASTp)
The necessary steps are the same for BLASTp and BLASTn (see Chapter 12: “Basic Local Alignment Search Tool for nucleotide (BLASTn)”), regarding:
- selection of sequence of interests (query sequences);
- specifying the BLAST program;
- selecting the sequence database;
- adjusting the optional parameters.
13.1.1 Open the BLASTp homepage
Open the URL: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi? PROGRAM = blastp&PAGE_TYPE = BlastSearch&LINK_LOC = blasthome to get the homepage for BLASTp.
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.
Read now
Unlock full access
More than 5,000 organizations count on O’Reilly
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.