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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 ==
| + | #[[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> |
| − | === Sequence similarity searches: queries and hits ===
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| − | | |
| − | === The BLAST database ===
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| − | | |
| − | === Aligning query and hit sequences === | |
| − | | |
| − | === Understanding the BLAST output ===
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| − | | |
| − | == Measuring BLAST hits ==
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| − | | |
| − | === Similarity: bitscores ===
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| − | | |
| − | === Significance: E-values ===
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| − | | |
| − | === Similarity vs. significance ===
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| − | | |
| − | == blastn vs. blastp ==
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| − | | |
| − | == Similarity, homology and orthology ==
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| − | | |
| − | == 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 ==
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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 ==
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| − | | |
| − | === The current directory === | |
| − | | |
| − | === The PATH ===
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| − | | |
| − | == 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 ==
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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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