Difference between revisions of "Ltr finder"
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|Ltr_fider}} | |{{#vardefine:app|Ltr_fider}} | ||
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | Xu, Zhao, and Hao Wang. “LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.” Nucleic Acids Research 35, suppl. 2 (2007): W265-W268. | |
|}} | |}} | ||
Latest revision as of 20:21, 15 August 2022
Description
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.
The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE, http://www.expasy.org/prosite/) to locate cores of important enzymes if they occur. Then possible ORFs are constructed based on that. At last, the program reports possible LTR retrotransposon models in different confidence levels according to how many signals and domains they hit.
Environment Modules
Run module spider Ltr_fider to find out what environment modules are available for this application.
System Variables
- HPC_LTR_FIDER_DIR - installation directory
- HPC_LTR_FIDER_BIN - executable directory
Citation
If you publish research that uses Ltr_fider you have to cite it as follows:
Xu, Zhao, and Hao Wang. “LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.” Nucleic Acids Research 35, suppl. 2 (2007): W265-W268.