Difference between revisions of "BLAT"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in template calls Required variables: app - lowercase name of the application e.g. "amber" url - url of the software page (project, company prod)
m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "")
Line 10: Line 10:
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
<!--Choose sections to enable - OPTIONAL-->
+
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->

Revision as of 17:52, 10 August 2012


Description

blat website  

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. BLAT (the BLAST-Like Alignment Tool) is a software program developed by Jim Kent at UCSC to identify similarities between DNA sequences and protein sequences. It was developed to assist in the annotation of the human genome sequence. BLAT is much faster than older tools such as BLAST for nucleotide and protein alignments, and it can also perform spliced alignments of RNA to DNA. BLAT uses a space-time tradeoff to compare sequences quickly. BLAT precomputes an index of all nonoverlapping k-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be similar to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible.

Required Modules

modules documentation

Serial

  • blat

System Variables

  • HPC_{{#uppercase:blat}}_DIR - installation directory
  • HPC_BLAT_BIN - executable directory
  • HPC_BLAT_DOC - documentation directory