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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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− | === Adjusting BLAST search parameters ===
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− | === Reducing the database size ===
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− | === Increasing the quality of the alignment ===
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− | === Using addition positional information ===
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− | === Adding query sequences ===
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− | == [[How to run BLAST|How to run BLAST]] ==
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− | === Running BLAST on the NCBI website ===
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− | === Running BLAST on the UoO Lifeportal ===
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− | === 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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− | === The current directory ===
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− | === The PATH ===
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− | == [[Running BLAST from the command-line|Running BLAST from the command-line]] ==
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− | === A simple BLAST search ===
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− | === 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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− | === Submit a BLAST search job script ===
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− | === Use “qlogin” to directly interact with Abel during job execution ===
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− | === Use the “freebee” system ===
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