Difference between revisions of "Last"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...") |
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Revision as of 14:29, 3 August 2012
Description
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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)
Running the application using 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.