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Contents
1
BLAST: the Basic Local Alignment Search Tool
1.1
BLAST for dummies
1.1.1
Sequence similarity searches: queries and hits
1.1.2
The BLAST database
1.1.3
Aligning query and hit sequences
1.1.4
Understanding the BLAST output
1.2
Measuring BLAST hits
1.2.1
Similarity: bitscores
1.2.2
Significance: E-values
1.2.3
Similarity vs. significance
1.3
blastn vs. blastp
1.4
Similarity, homology and orthology
1.5
Improving BLAST hits
1.5.1
Adjusting BLAST search parameters
1.5.2
Reducing the database size
1.5.3
Increasing the quality of the alignment
1.5.4
Using addition positional information
1.5.5
Adding query sequences
1.6
How to run BLAST
1.6.1
Running BLAST on the NCBI website
1.6.2
Running BLAST on the UoO Lifeportal
1.6.3
Running BLAST manually from the command line
1.7
Computer directories and the PATH
1.7.1
The current directory
1.7.2
The PATH
1.8
Running BLAST from the command-line
1.8.1
A simple BLAST search
1.8.2
Creating a custom BLAST database
1.9
General tips for using BLAST on Abel
1.9.1
Submit a BLAST search job script
1.9.2
Use “qlogin” to directly interact with Abel during job execution
1.9.3
Use the “freebee” system
BLAST: the Basic Local Alignment Search Tool
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
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