|
|
(6 intermediate revisions by the same user not shown) |
Line 1: |
Line 1: |
− | = [[BLAST_tutorial|BLAST tutorial]] =
| + | #<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]] ===
| |
− | | |
− | === [[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]] ===
| |
− | | |
− | === [[Running BLAST from the command-line#Creating a custom BLAST database|Creating a custom BLAST database]] === | |
− | | |
− | == [[General tips for using BLAST on Abel|General tips for using BLAST on Abel]] ==
| |
− | | |
− | === [[General tips for using BLAST on Abel#Submit a BLAST search job script|Submit a BLAST search job script]] ===
| |
− | | |
− | === [[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]] ===
| |
− | | |
− | === [[General tips for using BLAST on Abel#Use the .E2.80.9Cfreebee.E2.80.9D system|Use the “freebee” system]] ===
| |
− | | |
− | = [[PacBio_sequencing|PacBio sequencing]] =
| |