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= BLAST: the Basic Local Alignment Search Tool =
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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]] ===
 
 
 
=== Significance: E-values ===
 
 
 
=== Similarity vs. significance ===
 
 
 
== [[Blastn vs. blastp|blastn vs. blastp]] ==
 
 
 
== [[Similarity, homology and orthology|Similarity, homology and orthology]] ==
 
 
 
== [[Improving BLAST hits|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|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|Computer directories and the PATH]] ==
 
 
 
=== The current directory ===
 
 
 
=== The PATH ===
 
 
 
== [[Running BLAST from the command-line|Running BLAST from the command-line]] ==
 
 
 
=== A simple BLAST search ===
 
 
 
=== Creating a custom BLAST database ===
 
 
 
== [[General tips for using BLAST on Abel|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 ===
 

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