BLAST tutorial

From mn/ibv/bioinfwiki
Jump to: navigation, search

BLAST for dummies

Sequence similarity searches: queries and hits

The BLAST database

Aligning query and hit sequences

Understanding the BLAST output

Measuring BLAST hits

Similarity: bitscores

Significance: E-values

Similarity vs. significance

blastn vs. blastp

Similarity, homology and orthology

Improving BLAST hits

Adjusting BLAST search parameters

Reducing the database size

Increasing the quality of the alignment

Using addition positional information

Adding query sequences

How to run BLAST

Running BLAST on the NCBI website

Running BLAST on the UoO Lifeportal

Running BLAST manually from the command line

Computer directories and the PATH

The current directory

The PATH

Running BLAST from the command-line

A simple BLAST search

Creating a custom BLAST database

General tips for using BLAST on Abel

Submit a BLAST search job script

Use “qlogin” to directly interact with Abel during job execution

Use the “freebee” system