Difference between revisions of "Last"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "") |
Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
||
| Line 54: | Line 54: | ||
* 247 (EL6) | * 247 (EL6) | ||
<!-- --> | <!-- --> | ||
| − | {{#if: {{#var: mod}}|== | + | {{#if: {{#var: mod}}|==Execution Environment and Modules== |
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
Revision as of 02:03, 10 August 2012
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
Available versions
- 193 (EL5)
- 247 (EL6)
Execution Environment and Modules
To use last with the environment modules system at HPC the following commands are available:
Get module information for last:
$module spider last
Load the default application module:
$module load last
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_LAST_DIR - directory where last is located.