LTR_FINDER: Finding LTR Retrotransposons in Genome
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LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The size of input file is now limited to 50MB, and multiple sequences are allowed. Full descriptions on Input Data, Output Format and Parameters can be found in User's Manual [single-page HTML edition] [multiple-page HTML edition] [PDF edition].
Reference:   Zhao Xu, Hao Wang, "LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons", Nucleic Acids Res. 2007 July; 35(Web Server issue): W265-W268.
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Input Data:
File upload:
General Options:
Min LTR length      Max LTR length     
Min distance between LTRs      Max distance between LTRs     
Output score threshold          
Output format    Output with figure 
TG..CA restriction
Domain restriction
Other restriction    at least two of TSR,PBS and PPT
Auto mask highly repeated regions
Use ps_scan to predict IN(core), IN(c-term) and RH
  Predict PBS by using
which tRNA database
  Get result by e-mail
Advanced Options:
Length of exact match pairs      Extension max gap     
Sharpness higher threshold      Extension cutoff     
Sharpness lower threshold      Reliable extension     

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