|
|
(28 intermediate revisions by the same user not shown) |
Line 1: |
Line 1: |
− | = 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]] === | |
− | | |
− | === [[BLAST_for_dummies#The_BLAST_database|The BLAST database]] ===
| |
− | | |
− | === Aligning query and hit sequences ===
| |
− | | |
− | === Understanding the BLAST output ===
| |
− | | |
− | == [[Measuring BLAST hits|Measuring BLAST hits]] ==
| |
− | | |
− | === 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 ===
| |