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=== [[BLAST for dummies#Sequence similarity searches: queries and hits|Sequence similarity searches: queries and hits]] ===
 
=== [[BLAST for dummies#Sequence similarity searches: queries and hits|Sequence similarity searches: queries and hits]] ===
  
=== [[BLAST_for_dummies#The_BLAST_database|The BLAST database]] ===
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=== [[BLAST for dummies#The BLAST database|The BLAST database]] ===
  
=== [[BLAST_for_dummies#Aligning_query_and_hit_sequences|Aligning query and hit sequences]] ===
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=== [[BLAST for dummies#Aligning query and hit sequences|Aligning query and hit sequences]] ===
  
=== [[BLAST_for_dummies#Understanding_the_BLAST_output|Understanding the BLAST output]] ===
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=== [[BLAST for dummies#Understanding the BLAST output|Understanding the BLAST output]] ===
  
 
== [[Measuring BLAST hits|Measuring BLAST hits]] ==
 
== [[Measuring BLAST hits|Measuring BLAST hits]] ==
  
=== [[Measuring_BLAST_hits#Similarity:_bitscores|Similarity: bitscores]] ===
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=== [[Measuring BLAST hits#Similarity: bitscores|Similarity: bitscores]] ===
  
=== [[Measuring_BLAST_hits#Significance:_E-values|Significance: E-values]] ===
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=== [[Measuring BLAST hits#Significance: E-values|Significance: E-values]] ===
  
=== [[Measuring_BLAST_hits#Similarity_vs._significance.C2.A0|Similarity vs. significance]] ===
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=== [[Measuring BLAST hits#Similarity vs. significance.C2.A0|Similarity vs. significance]] ===
  
 
== [[Blastn vs. blastp|blastn vs. blastp]] ==
 
== [[Blastn vs. blastp|blastn vs. blastp]] ==
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== [[Improving BLAST hits|Improving BLAST hits]] ==
 
== [[Improving BLAST hits|Improving BLAST hits]] ==
  
=== [[Improving_BLAST_hits#Adjusting_BLAST_search_parameters|Adjusting BLAST search parameters]] ===
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=== [[Improving BLAST hits#Adjusting BLAST search parameters|Adjusting BLAST search parameters]] ===
  
=== [[Improving_BLAST_hits#Reducing_the_database_size|Reducing the database size]] ===
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=== [[Improving BLAST hits#Reducing the database size|Reducing the database size]] ===
  
=== [[Improving_BLAST_hits#Increasing_the_quality_of_the_alignment|Increasing the quality of the alignment]] ===
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=== [[Improving BLAST hits#Increasing the quality of the alignment|Increasing the quality of the alignment]] ===
  
=== [[Improving_BLAST_hits#Using_addition_positional_information|Using addition positional information]] ===
+
=== [[Improving BLAST hits#Using addition positional information|Using addition positional information]] ===
  
=== [[Improving_BLAST_hits#Adding_query_sequences|Adding query sequences]] ===
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=== [[Improving BLAST hits#Adding query sequences|Adding query sequences]] ===
  
 
== [[How to run BLAST|How to run BLAST]] ==
 
== [[How to run BLAST|How to run BLAST]] ==
  
=== [[How_to_run_BLAST#Running_BLAST_on_the_NCBI_website|Running BLAST on the NCBI website]] ===
+
=== [[How to run BLAST#Running BLAST on the NCBI website|Running BLAST on the NCBI website]] ===
  
=== [[How_to_run_BLAST#Running_BLAST_on_the_UoO_Lifeportal|Running BLAST on the UoO Lifeportal]] ===
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=== [[How to run BLAST#Running BLAST on the UoO Lifeportal|Running BLAST on the UoO Lifeportal]] ===
  
=== [[How_to_run_BLAST#Running_BLAST_manually_from_the_command_line|Running BLAST manually from the command line]] ===
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=== [[How to run BLAST#Running BLAST manually from the command line|Running BLAST manually from the command line]] ===
  
 
== [[Computer directories and the PATH|Computer directories and the PATH]] ==
 
== [[Computer directories and the PATH|Computer directories and the PATH]] ==
  
=== [[Computer_directories_and_the_PATH#The_current_directory|The current directory]] ===
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=== [[Computer directories and the PATH#The current directory|The current directory]] ===
  
=== [[Computer_directories_and_the_PATH#The_PATH|The PATH]] ===
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=== [[Computer directories and the PATH#The PATH|The PATH]] ===
  
 
== [[Running BLAST from the command-line|Running BLAST from the command-line]] ==
 
== [[Running BLAST from the command-line|Running BLAST from the command-line]] ==
  
=== [[Running_BLAST_from_the_command-line#A_simple_BLAST_search|A simple BLAST search]] ===
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=== [[Running BLAST from the command-line#A simple BLAST search|A simple BLAST search]] ===
  
=== [[Running_BLAST_from_the_command-line#Creating_a_custom_BLAST_database|Creating a custom BLAST database]] ===
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=== [[Running BLAST from the command-line#Creating a custom BLAST database|Creating a custom BLAST database]] ===
  
 
== [[General tips for using BLAST on Abel|General tips for using BLAST on Abel]] ==
 
== [[General tips for using BLAST on Abel|General tips for using BLAST on Abel]] ==
  
=== [[General_tips_for_using_BLAST_on_Abel#Submit_a_BLAST_search_job_script|Submit a BLAST search job script]] ===
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=== [[General tips for using BLAST on Abel#Submit a BLAST search job script|Submit a BLAST search job script]] ===
  
=== [[General_tips_for_using_BLAST_on_Abel#Use_.E2.80.9Cqlogin.E2.80.9D_to_directly_interact_with_Abel_during_job_execution|Use “qlogin” to directly interact with Abel during job execution]] ===
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=== [[General tips for using BLAST on Abel#Use .E2.80.9Cqlogin.E2.80.9D to directly interact with Abel during job execution|Use “qlogin” to directly interact with Abel during job execution]] ===
  
=== [[General_tips_for_using_BLAST_on_Abel#Use_the_.E2.80.9Cfreebee.E2.80.9D_system|Use the “freebee” system]] ===
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=== [[General tips for using BLAST on Abel#Use the .E2.80.9Cfreebee.E2.80.9D system|Use the “freebee” system]] ===
 +
 
 +
= [[PacBio_sequencing|PacBio sequencing]] =

Revision as of 14:05, 9 March 2015

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

PacBio sequencing