---
title: "QuickBLASTP – Rapidly Find High-Scoring Protein Matches"
output: html_notebook
---

## What is QuickBLASTP?

This is a program for rapidly finding high scoring matches on large databases at least 10X faster than ordinary BLAST. 

It is a faster alternative for ordinary protein-protein blast. 

It uses specially pre-indexed database.

It is designed for rapid matching of queries and *very similar* database sequences. 

Less sensitive.

## What is QuickBLASTP?

• A faster alternative for ordinary protein-protein BLAST

• Uses a specially pre-indexed database

• Rapid matching of queries and very similar database sequences

• 97% of the database sequences with 70% or more identity to query

• 98% of the database sequences with 80% or more identity to query

Need for a process to quickly find strong matches to a set of query sequences. Sensitivity less important.

## QuickBLASTP Strategy (Oversimplified)

• First Part

Find candidate matches using an alignment-free method (index of 5-mers
from database and query sequences) to find candidate matches.

• Second Part

 Align top 1,500 candidates and query matches using **blastp** 
 
 Standard **blastp** alignments and statistics

## Availability

• *SmartBLAST* has used the QuickBLASTP algorithm for several years.

• *QuickBLASTP* now on protein-protein BLAST page as a program choice.

• *kblastp* standalone demonstration package on the BLAST FTP area.

## Programs in Demo Release

• *kblastp* - search program 

Parallel options to **blastp**

• *mkkblastindex* - database indexing program

Takes a formatted protein database as input

 Adds additional indices needed for initial alignment-free search

## Programs in Demo Release

• *update_blastdb.pl* - script for downloading NCBI BLAST databases 

• *catvolumes.sh* -script to load BLAST DB volumes into memory

Speeds up search to load large database and indices into memory prior to first search

Written for *refseq_protein* (modify for other databases)

## Important considerations

• QuickBLASTP (**kblastp**) rapidly finds closely related proteins 

• Not useful below about 65% identity

• Best used for batches of queries 

• Standalone **kblastp**

• Maximum speedup requires that the BLAST database plus the indices be completely
loaded into RAM

• NOTE: nr plus indices require 200 - 250 Gigabytes of RAM. The **kblastp** index files occupy more than half of this.


## References

https://ncbiinsights.ncbi.nlm.nih.gov/2018/01/26/new-videos-youtube-ncbi-resources-quickblastp-update-api-keys-eutils/

https://www.ncbi.nlm.nih.gov/books/NBK1734/
