TE nest Download

TE nest Instructions

• TE nest: Transposable Element Annotation:
  TE nest (TE nest) searches your input sequence against the chosen repeat database to identify nested TE insertions. TE nest will output coordinates of the TE annotations, and input these annotations to svg_ltr to provide a display showing the chronological order of the nested insertions.
  
• svg_ltr: Transposable Element Insertion Display:
  svg_ltr (svg_ltr) gives the ability to separately run the display on TE nest annotation files.
  
• LTR Retrotransposon Insertion Age:
  TE nest calculates the age since insertion of LTR retrotransposons. This calculation is based on the sequence difference between the left and right LTRs, when a LTR retrotransposon inserts into the genome the LTRs are identical, over evolution the LTRs accumulate mutations. The rate of these mutations (rate)(ref) is used to calculate the LTR retrotransposon time since insertion (insert calculation).
  
• TE Database Submission:
  TE database submission is not yet online. Contact me for more information.

• Sequence Input:
  Input a DNA sequence into the submission box, or upload a sequence. Your input sequence can be in fasta format (with a '>header') or simply a plain DNA sequence. This sequence should be in a flatfile format, with no trailing tabs or spaces after each line.
• Repeat Database:
  Pick a repeat database from the pull down menu. Alternatively you can choose to build a custom repeat database.
  To use a custom repeat database:
  • Select 'custom' from the repeat database pull down menu.
  • Upload the three repeat database files. In each case, a multi-sequence fasta file is required. This database needs to be 'unique' in that a consensus sequence for each repeat family type, or a representitive of each repeat type is to be entered. In rare cases using 2-3 entries for a very divergent TE family is acceptable. The header of each sequence will become the name of the repeat. This repeat name must not contain spaces and case must be the same for each time it is entered. For example, an LTR retrotransposon will have three sequence entries and one TE list entry; the LTR file, the retrotransposon file, the TE file, and the TE list. In each entry the name (header) must be the same.
  • LTR retrotransposon sequence file: One sequence entry for each type of LTR retrotrasnposon.
  • LTR sequence file: A single LTR of each LTR retrotransposon entered into the LTR retrotransposon file.
  • TE sequence file: All TE sequences to be identified. This includes LTR retrotransposons, non-LTR retrotransposons, DNA transposons, etc.
  • Enter or upload a te_list file
• TE list:
  TE nest uses the TE list to find TE annotations in the input sequence. Customization of the TE list can be used to optimize TE annotations by selecting or de-selecting certain elements from a provided repeat database. To make a custom TE list, paste in one of the following organism TE lists, and change to fit your TE nest run. First column is name of TE, second column is TE type; 0 for LTR retrotransposon, 1 for any other type. LTR retrotransposons (0) must be at the top of the list.
  Maize TE list
  Rice TE list
  Barley TE list
  Wheat TE list
• TE nest Program Parameters:
  TE nest allows customization with the following options:
  • Alignment Options:
  Alignment options are found three times, once for solo LTRs (SOLOs), once for LTR retrotransposon middle regions (MIDs), and once for fragmented or whole non-LTR transposons (FRAG/NLTR). Each of these sections has the same alignment options, although with different default values. Gap open penalty and gap extension penalty allow for opening and extending gaps in the alignment. Alignments reported is how many alignment pieces TE nest will evalulate, raising this value may find small missing segments, but will greatly increase the runtime of TE nest. Alignment minimum score is the cutoff value for alignments to use.
• Output Options and Formats:
  Select from the three TE nest output formats:
  • Annotation table (*.LTR file).
  The annotation table is the main output of TE nest, giving coordinates for each identified nested TE. The four annotation types; SOLO (solo LTRs), PAIR (full LTR retrotransposons), FRAG (fragmented TEs of all types), NLTR (Full length non-LTR containing TEs). Each the SOLO, FRAG, and NLTR annotation types follow the same format, one header line and one coordinate line (shown below) per TE annotation. The PAIR annotation type contains four lines per TE; one header line, one left LTR coordinate line, one right LTR coordinate line, one middle region LTR line (shown below).
  
  

  Example TE nest *.LTR annotation file:	Explanation:
  33610	Sequence length
  input.fasta	input sequence name
  SOLO s0 milt 1 0 20 0	Solo entry, solo number, type, direction, nest group, nest order, nest level
  s0 100 276 1 176 662 1140 177 656	Solo number, Sequence start, seq end, TE start, TE end, -gap- etc.
  SOLO s1 gyma 0 0 32 0
  s1 1620 5918 1 4198
  PAIR p0 danelle 0 0.030 41 41 0	Pair entry, pair number, type, direction, BSR, nest group, nest order, nest level
  p0 L 8710 13312 1 4602	Pair number, Left LTR, seq start, seq end, TE start, TE end
  p0 R 19507 24778 1 4601	Pair number, Right LTR, seq start, seq end, TE start, TE end
  p0 M 13313 19506 4603 10796	Pair number, Middle region, seq start, seq end, TE start, TE end
  PAIR p1 opie 0 0.023 39 39 0
  p1 L 6152 6280 1 128 8391 8709 260 577 24107 24778 580 1251
  p1 R 31184 32427 1 1243
  p1 M 24779 31183 1266 7670
  FRAG f0 dagaf 0 1 1 0	Frag entry, frag number, type, direction, nest group, nest order, nest level
  f0 6281 8390 3256 5366	Frag number, Sequence start, seq end, TE start, TE end, -gap- etc.
  FRAG f1 grande 0 5 5 0
  f1 25203 26653 1 1450 27748 33610 1444 7306
  NLTR n0 cacta 0 27 21 1	Non-LTR entry, NLTR number, type, direction, nest group, nest order, nest level
  n0 26654 27747 1 1094	NLTR number, Sequence start, seq end, TE start, TE end, -gap- etc.
  NLTR n1 isb 0 27 17 1
  n1 277 661 1 384

  • SVG TE insertion display (*.svg file).
  The SVG output gives the graphical nesting display. svg_ltr is a separate program that uses the annotation coordinates file to produce the picture of nested TEs. This file is scalable vector graphic (SVG) format, viewable in the latest firefox version. A vector graphic format is used to give resizing abilities without losing quality. The SVG display is automatically made with a TE nest sequence input, and can also be re-run by inputting the *.LTR annotation file (svg_ltr Display)
  
  
  
  • Repeat masked fasta sequence (*.mask file).
  TE nest can also output the original sequence file with all annotated TEs masked out with Ns. This gives the user the ability to input the masked sequence into gene prediction programs.

• Annotation Input:
  Input or upload the *.LTR annotation file, the output of TE nest. You can use this separate svg_ltr input to rebuild the insertion nesting display, or alter coordinates on the annotation output and make a new display. You can also use this function to display TE insertions not identified with TE nest, arrange your coordinates in the *.LTR annotation format (TE nest output formats).
• svg_ltr Display Subset of Annotations:
A subset of the input sequence can be displayed with svg_ltr. Input the whole annotation file and enter the start and stop coordinates of interest. The coordinate window may intersect TE annotations, you can select to either show these cut insertions as fragments (check the split coordinates box) or to not display the cut off TEs (deselect the box).
• svg_ltr Program Parameters:
svg_ltr allows customization of the TE nest display by selecting the following options:
• Display Options:
You can select to display different types of TE nest annotations. Select or deselect paired LTR Retrotransposons (PAIRs), solo LTRs (SOLOs), whole non-LTR TEs (NLTRs), or fragmented TEs (FRAGs). At least one check box must be selected.
• White Out Options:
TE nest displays unidentified 'unique' regions found within TE annotations as white triangles to show the regions does not match the TE sequence. Display of the white region is usefull for identification of unknown TEs, incomplete TE annotations in the database, or areas of rearrangements. This option can be turned on or off.
• Legend Options:
The legend at the bottom of the svg_ltr display can be customized in the following manner. The default width of TE names in the legend is 5, this can be shortened or lengthened for different sized TE displays. The scale bar length can be changed, helpful for longer input sequences. The number of tic marks within the scale bar can be altered.
• Coordinate Options:
Coordinates of TE annotations can be displayed on the insertion display. Two types of coordinates are available TE based coordinates show coordinates of the TE insertions relative to the consensus sequence database TE. Input sequence based coordinates show the TE insertions relative to the coordinates of the DNA sequence. Furthermore, each data type can be turned on or off. Select from PAIRs, SOLOs, FRAGs, or NLTRs to show any of these TE coordinates.
• Insertion Age Options:
Either age since insertion in million years ago (MYA) or the substitution rate between the left and right LTR can be shown in the box within paired LTR retrotransposons.