Difference between revisions of "Last"
Jump to navigation
Jump to search
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software | + | [[Category:Software]][[Category:Biology]][[Category:Alignment]][[Category:Sequencing]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|last}} | |{{#vardefine:app|last}} | ||
| Line 35: | Line 35: | ||
* Do spliced alignment | * Do spliced alignment | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 57: | Line 55: | ||
WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
| − | |||
| − | |||
Latest revision as of 19:29, 12 August 2022
Description
LAST finds similar regions between sequences.
What distinguishes LAST from BLAST and similar tools (e.g. BLAT, LASTZ, YASS)? The main difference is that it copes more efficiently with repeat-rich sequences (e.g. genomes). For example, it can align reads to genomes without repeat-masking and without becoming overwhelmed by repetitive hits.
LAST can:
- Handle big sequence data, e.g:
- Compare two vertebrate genomes
- Align billions of DNA reads to a genome
- Indicate the reliability of each aligned column.
- Use sequence quality data properly.
- Compare DNA to proteins, with frameshifts.
- Compare PSSMs to sequences
- Calculate the likelihood of chance similarities between random sequences.
LAST cannot (yet):
- Do spliced alignment
Environment Modules
Run module spider last to find out what environment modules are available for this application.
System Variables
- HPC_LAST_DIR - installation directory