Difference between revisions of "Last"

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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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[[Category:Software]][[Category:Bioinformatics]][[Category:Biology]][[Category:Alignment]][[Category:Sequencing]]
 
{|<!--Main settings - REQUIRED-->
 
{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|last}}
 
|{{#vardefine:app|last}}
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* Do spliced alignment
 
* Do spliced alignment
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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WRITE CITATION HERE
 
WRITE CITATION HERE
 
|}}
 
|}}
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 17:51, 10 June 2022

Description

last website  

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