Difference between revisions of "BLAT"
Moskalenko (talk | contribs) m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "") |
|||
| (17 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|blat}} | |{{#vardefine:app|blat}} | ||
|{{#vardefine:url|http://genome.ucsc.edu/goldenPath/help/blatSpec.html}} | |{{#vardefine:url|http://genome.ucsc.edu/goldenPath/help/blatSpec.html}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
| − | |||
| − | |||
| − | |||
| − | |||
|{{#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--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| Line 49: | Line 34: | ||
boundaries that have canonical splice sites where feasible. | boundaries that have canonical splice sites where feasible. | ||
| − | + | <!--Modules--> | |
| − | + | ==Environment Modules== | |
| − | <!-- --> | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
* HPC_BLAT_BIN - executable directory | * HPC_BLAT_BIN - executable directory | ||
* HPC_BLAT_DOC - documentation directory | * HPC_BLAT_DOC - documentation directory | ||
| − | {{#if: {{#var: exe}}|== | + | <!--Additional--> |
| − | + | {{#if: {{#var: exe}}|==Additional Information== | |
| + | '''Note:''' If you encounter segfaults (crashes) while running blat against a larger reference database like nr or md5nr please use a three-way split version of the respective database under <code>/bio/reference/fasta</code> and run three blat processes instead of one. The upstream author Jim Kent has been notified of the issue. It's unknown when a fix will be provided. | ||
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 13:03, 15 August 2022
Description
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.
Environment Modules
Run module spider blat to find out what environment modules are available for this application.
System Variables
- HPC_BLAT_DIR - installation directory
- HPC_BLAT_BIN - executable directory
- HPC_BLAT_DOC - documentation directory
Additional Information
Note: If you encounter segfaults (crashes) while running blat against a larger reference database like nr or md5nr please use a three-way split version of the respective database under /bio/reference/fasta and run three blat processes instead of one. The upstream author Jim Kent has been notified of the issue. It's unknown when a fix will be provided.