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− | = BLAST: the Basic Local Alignment Search Tool =
| + | #<span style="font-size:large;">[[BLAST tutorial|BLAST tutorial]]</span> |
− | | + | #<span style="font-size:large;">[[PacBio sequencing|PacBio sequencing]]</span> |
− | == [[BLAST for dummies|BLAST for dummies]] ==
| + | #[[RNASeq_and_differential_gene_expression_analysis|<span style="font-size:large;">RNASeq and differential gene expression analysis</span>]] |
− | | + | #<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]] ===
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− | === [[BLAST_for_dummies#The_BLAST_database|The BLAST database]] ===
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− | === [[BLAST_for_dummies#Aligning_query_and_hit_sequences|Aligning query and hit sequences]] ===
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− | === [[BLAST_for_dummies#Understanding_the_BLAST_output|Understanding the BLAST output]] ===
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− | == [[Measuring BLAST hits|Measuring BLAST hits]] ==
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− | === [[Measuring_BLAST_hits#Similarity:_bitscores|Similarity: bitscores]] ===
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− | === [[Measuring_BLAST_hits#Significance:_E-values|Significance: E-values]] ===
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− | | |
− | === [[Measuring_BLAST_hits#Similarity_vs._significance.C2.A0|Similarity vs. significance]] ===
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− | == [[Blastn vs. blastp|blastn vs. blastp]] ==
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− | == [[Similarity, homology and orthology|Similarity, homology and orthology]] ==
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− | == [[Improving BLAST hits|Improving BLAST hits]] ==
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− | === [[Improving_BLAST_hits#Adjusting_BLAST_search_parameters|Adjusting BLAST search parameters]] ===
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− | === [[Improving_BLAST_hits#Reducing_the_database_size|Reducing the database size]] ===
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− | === [[Improving_BLAST_hits#Increasing_the_quality_of_the_alignment|Increasing the quality of the alignment]] ===
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− | === [[Improving_BLAST_hits#Using_addition_positional_information|Using addition positional information]] ===
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− | === [[Improving_BLAST_hits#Adding_query_sequences|Adding query sequences]] ===
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− | == [[How to run BLAST|How to run BLAST]] ==
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− | === [[How_to_run_BLAST#Running_BLAST_on_the_NCBI_website|Running BLAST on the NCBI website]] ===
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− | === [[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_manually_from_the_command_line|Running BLAST manually from the command line]] ===
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− | == [[Computer directories and the PATH|Computer directories and the PATH]] ==
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− | === [[Computer_directories_and_the_PATH#The_current_directory|The current directory]] ===
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− | === [[Computer_directories_and_the_PATH#The_PATH|The PATH]] ===
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− | == [[Running BLAST from the command-line|Running BLAST from the command-line]] ==
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− | === [[Running_BLAST_from_the_command-line#A_simple_BLAST_search|A simple BLAST search]] ===
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− | === [[Running_BLAST_from_the_command-line#Creating_a_custom_BLAST_database|Creating a custom BLAST database]] ===
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− | == [[General tips for using BLAST on Abel|General tips for using BLAST on Abel]] ==
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− | === [[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#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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− | === Use the “freebee” system ===
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