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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]] ===
 
 
 
=== [[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]] ===
 
 
 
=== 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