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= [[BLAST_tutorial|BLAST tutorial]] =
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#<span style="font-size:large;">[[BLAST tutorial|BLAST tutorial]]</span>
 
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#<span style="font-size:large;">[[PacBio sequencing|PacBio sequencing]]</span>
== [[BLAST for dummies|BLAST for dummies]] ==
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#[[RNASeq_and_differential_gene_expression_analysis|<span style="font-size:large;">RNASeq and differential gene expression analysis</span>]]
 
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#<span style="font-size:large;">[[Amplicon sequencing|Amplicon sequencing]]</span>
=== [[BLAST for dummies#Sequence similarity searches: queries and hits|Sequence similarity searches: queries and hits]] ===
 
 
 
=== [[BLAST for dummies#The BLAST database|The BLAST database]] ===
 
 
 
=== [[BLAST for dummies#Aligning query and hit sequences|Aligning query and hit sequences]] ===
 
 
 
=== [[BLAST for dummies#Understanding the BLAST output|Understanding the BLAST output]] ===
 
 
 
== [[Measuring BLAST hits|Measuring BLAST hits]] ==
 
 
 
=== [[Measuring BLAST hits#Similarity: bitscores|Similarity: bitscores]] ===
 
 
 
=== [[Measuring BLAST hits#Significance: E-values|Significance: E-values]] ===
 
 
 
=== [[Measuring BLAST hits#Similarity vs. significance.C2.A0|Similarity vs. significance]] ===
 
 
 
== [[Blastn vs. blastp|blastn vs. blastp]] ==
 
 
 
== [[Similarity, homology and orthology|Similarity, homology and orthology]] ==
 
 
 
== [[Improving BLAST hits|Improving BLAST hits]] ==
 
 
 
=== [[Improving BLAST hits#Adjusting BLAST search parameters|Adjusting BLAST search parameters]] ===
 
 
 
=== [[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]] ===
 
 
 
=== [[Improving BLAST hits#Using addition positional information|Using addition positional information]] ===
 
 
 
=== [[Improving BLAST hits#Adding query sequences|Adding query sequences]] ===
 
 
 
== [[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 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]] ===
 
 
 
== [[Computer directories and the PATH|Computer directories and the PATH]] ==
 
 
 
=== [[Computer directories and the PATH#The current directory|The current directory]] ===
 
 
 
=== [[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#A simple BLAST search|A simple BLAST search]] ===
 
 
 
=== [[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#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]] ===
 
 
 
=== [[General tips for using BLAST on Abel#Use the .E2.80.9Cfreebee.E2.80.9D system|Use the “freebee” system]] ===
 
 
 
= [[PacBio_sequencing|PacBio sequencing]] =
 

Latest revision as of 12:51, 24 August 2015

  1. BLAST tutorial
  2. PacBio sequencing
  3. RNASeq and differential gene expression analysis
  4. Amplicon sequencing