news and updates
05.07.16 | maintenance 20.06.11 | service is up
background and instructions
| intro LTRphyler is a compendium of tools for the detection and analysis of LTR retrotransposons in DNA sequences, including coding domain detection with Wise2, tree construction with MAFFT, sequence relationship analysis and visualisation with Circoletto. Behind it, we have placed a database of more than 3300 LTR retrotransposons from more than 660 species parsed from ICTVdb and RepBase from four different taxonomic categories: arthropoda, fungi, plants, and vertebrates. | input format and options Input is a FASTA-formatted nucleotide sequence, which you should suspect contains an LTR retrotransposon, or part of it for that matter. Also, you have to select the taxonomy of your sequence from arthropoda, fungi, plants, and vertebrates - this will allow us to be more specific and accurate about what we provide back. | results After you submit, you move to the results page where you will be kept informed of the progress of LTRphyler, including: the health of your sequence(s), the detection of the integrase and reverse transcriptase coding domains, with details of alignment length and coordinates, the tree building for all coding domains detected in exemplars and your sequences, the run of Circoletto, essentially BLASTn and tBLASTx, against our LTR retrotransposon database, any errors or advice at any stage. A list of available files is then produced, which depending on what happened, might include: FASTA-formatted sequences of the detected coding domains in your query, trees of coding domains detected in exemplars and your sequences, downloadable or applet viewable, BLASTn and tBLASTx outputs in HTML formats, our LTR retrotransposon database IDs and related information, Circoletto visualisation of the BLAST results, label changes Circoletto might have made. In the Circoletto visualisation, the database entries have been pre-processed and their LTRs and coding domains colour-coded, LTR=redish, integrase=purple, reverse transcriptase=lime or green, for Copia or Gypsy respectively. The coding domains, if any, are also colour-coded on your query. Ribbons are grey by default, unless there is meaningful overlap with colour-coded regions on the database entries, in which case the ribbons "borrow" that colour so that you can follow more easily. The Circoletto help section has more information for you.
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