TE nest: Annotation and Display of Nested Transposable Elements

Run TE nest

TE Nest is temporarily unavailable while we upgrade BLAST components. We apologize for the inconvenience. Please contact us if you would like us to notify you when the tool is back in service [April 23, 2009].

Input Sequence in FASTA format Instructions

(500Kb limit)
Email address for result files (REQUIRED).

Submit for TE nest annotation and display with default options.


- OR -

optimize TE nest annotations and display with choices below.



or upload sequence file in FASTA format:

Options

Repeat Database Instructions

Select Repeat Database: OR Enter Custom Repeat Database:

If entering a custom repeat database you must select custom in the pull-down menu
to the left, enter all three files below, and enter a custom TE list in next section.

upload LTR file:
upload LTR retro file:
upload TE file:


TE list Instructions

Default TE list OR Custom TE list

Input Custom TE list

or upload custom TE list:

Options Instructions

LTR Options:
LTR gap open penalty
LTR gap extension penalty
LTR alignments reported
LTR alignment minimum score
LTR overlap allowed in recombination
LTR overlap unique coordinates
LTR powerset offset
LTR smallest size
LTR powerset gap division
LTR powerset max size, in Kb

LTR Pairing Options:
Amount to incremently drop for LTR comparison




Middle Region Options:
MID gap open penalty
MID gap extension penalty
MID alignments reported
MID alignment minimum score




non-LTR and Fragmented Transposon Options:
F/N gap open penalty
F/N gap extension penalty
F/N alignments reported
F/N alignment minimum score




Output Options:    Instructions
Annotation table (required for svg_ltr display)
Masked fasta file
SVG display file:



SVG Display Options

Instructions
Display Options:
Show Paired LTR Retrotransposon Insertions
Show Solo LTRs
Show Whole non-LTR Transposons
Show Fragmented TE Insertions

White Out Options:
Show Unidentified Areas Within TEs as White Regions

Legend Options:
Amount of TEs Listed Across (Horizontally) in Legend
Length in Kb of Scale Bar
Number of Vertical Tic Marks in Scale Bar
 Coordinate Options:

Coordinates:
 Off
TE Based
Sequence Based
     Paired LTR Retrotransposon Coordinates
     Solo LTR Coordinates
     non-LTR Transposon Coordinates
     Fragmented TE Coordinates

Time Since Insertion:
Million Years Ago
Base Pair Substitution Rate

   Clicking the submit button will send you a table of TE annotations. Depending on the repetitive content this may
   take 5 minutes to a hour or more. Annotation and display results will be emailed to the address entered above.
   You must use Firefox version 1.5 or later to view the SVG output.
Brent A. Kronmiller, 2006 bak@iastate.edu.

Brent's homepage: bak
Wiselab homepage: wiselab