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This readme should help you get started with clariTE.pl, which is for TE annotation

Setting up -------------------------------------------------------------------

i) Using clariTE.pl

clariTE.pl is a program that post process the xm output file of RepeatMasker.

ii) Usage

clariTE.pl -fasta -LTR -classi -gene

Command line example : clariTE.pl -LTR clariTeRep_LTRposition.txt -gene v443_0001.annoGene.embl -classi clariTeRep_classification.txt -fasta v443_0001.fas -dir [your directory] v443_0001.fas.out.xm


To recap, clariTE.pl requires:

  • the output file .xm from RepeatMasker
  • a tabular file containing the classification of the library use in RepeatMasker :
  • a tabular file containing the position of the LTR retrotransposons present in the library
  • embl file containing the gene annotation of the sequence (in triAnnot format).
  • a FASTA-format file containing your query sequence (multi-FASTA file is not accepted)

iv) Input FILE

1) xm output file from RepeatMasker

example :

1725 20.7 2.6 0.8 v443_2791 5 393 (40687) C ctgB_rep_0246#Unknown (7481) 396 1 * 4791 21.8 0.8 3.3 v443_2791 378 1704 (39376) + ctgF_rep_0077#Unknown 322 1615 (7557) * 5649 11.4 0.4 0.4 v443_2791 799 1704 (39376) + ctgF_rep_0055#Unknown 722 1627 (11086) 15719 9.1 0.5 0.7 v443_2791 6858 9147 (31933) + ctgF_rep_0055#Unknown 5829 8115 (4598) 9263 22.2 0.9 2.8 v443_2791 7600 9932 (31148) + ctgF_rep_0077#Unknown 2241 4528 (4644) *

2) Tabular file of the classification

example :

sequenceID family

TREP100 RLC_famc1.1 TREP1000 DTT_famn14 TREP1001 DTT_famn1

3) Tabular file of the position of LTR in the LTR retrotransposons Note : the total number of LTR retrotransposons is not obligated to be present in this file.

example :

sequenceID family LTRtype start end

ctgH_rep_0307 RLG_famc3 LTR5 1 3945 ctgH_rep_0307 RLG_famc3 LTR3 7931 12091 sr2_rep_0226 RLC_famc9 LTR5 1 214 sr2_rep_0226 RLC_famc9 LTR3 4972 5185

4) Gene annotation in EMBL format TriAnnot Note : only the locus_tag and the id is require to run clariTE.pl, other tag (such as blastp_file...) are not necessary.

example :

ID unknown; SV 1; linear; unassigned DNA; STD; UNC; 1411106 BP. XX AC unknown; XX XX FT CDS join(141960..142006,142121..142147,142248..142370,142493..142739,142850..142873) FT /locus_tag=v443_0002_EXONERATE_BLASTX_protOSA_6 FT /blastp_file=v443_0002_EXONERATE_BLASTX_protOSA_141960_142873_Q5JM42_Match_0005_mRNA_CDS.bltp FT /id=v443_0002_EXONERATE_BLASTX_protOSA_141960_142873_Q5JM42_Match_0005_mRNA_joinedCDS FT /note=Similar_to: hypothetical_protein FT /note=BestBlastHit: B9EZI3_ORYSJ TrEMBL databank Putative uncharacterized protein - %25id: 91.67 - hcov: 13.78 - qcov: 100.00 FT /note=Status: High Confidence FT CDS complement(join(143435..144154,144239..144363,145030..145267)) FT /locus_tag=v443_0002_EXONERATE_BLASTX_validated_9 FT /expressed FT /blastp_file=v443_0002_EXONERATE_BLASTX_validated_143435_145267_AFR_02_CAT01_3_Match_0001_mRNA_CDS.bltp FT /id=v443_0002_EXONERATE_BLASTX_validated_143435_145267_AFR_02_CAT01_3_Match_0001_mRNA_joinedCDS FT /note=Similar_to: putative_function - F2CSA4_HORVD TrEMBL databank Predicted protein OS Hordeum vulgare var distichum PE 2 SV 1 FT /note=BestBlastHit: F2CSA4_HORVD TrEMBL databank Predicted protein - %25id: 96.12 - hcov: 100.56 - qcov: 100.00 FT /note=Function_coverage: 94.71 FT /note=Function_identity: 97.94 FT /note=Function_target: F2CSA4 22 361 FT /note=Status: High Confidence

5) FASTA file Note : only one sequence could be contained it the FASTA file, multi fasta file are accepted

v) Help


CREATED: 2012-05-31

LAST MODIF: 01/02/2014

AUTHOR: Josquin Daron (INRA Clermont-Ferrand)


This script is used to post process a embl output of RepeatMasker

USAGE: clariTE.pl -fasta -LTR -classi -gene

   ### OPTIONS ###

   -h|--help:             print this help
   -LTR:                  tabulation file of the LTR annotations
   -classi:               corresponding file sequence id to family id
   -fasta:                fasta file of the annotated sequence
   -gene:                 embl file of the gene annotation
   -dir:                  directory name
   -v:                    verbosity (3,4)

vi) Output format


--> read all input File --> step overlaping feature --> step merge collinear feature --> step Join --> /home/v443_0001.fas_annoTE.embl embl file created --> failure is not an option

2) In embl file

Example embl output :

ID unknown; SV 1; linear; unassigned DNA; STD; UNC; 1411106 BP. XX AC unknown; XX XX FH Key Location/Qualifiers FH FT repeat_region complement(join(10..373,1824..2754)) FT /parent=mp1 # parent id FT /status=fragmented # status of the predicton (complete or fragmented) FT /range=3854..4785,4881..5242, # position on the reference sequence used to annotated the prediction FT /post=RLG_famc36 8671bp 3854..5242 # tag FT /compo=RLG_famc36 100.00 # composition of the prediction FT /id=3_v443_0001 # id of the prediction FT /copie=ctgD_rep_0264 # sequenceID in the library used to annotated the prediction

vii) Licence

Copyright or or Copr. Josquin Daron INRA-GDEC 01/09/2014

email: josquin.daron@clermont.inra.fr

This software is a computer program whose purpose is to predict Transposable Elements (TEs) in complexe genome such as wheat. The program correct raw similarity search result from RepeatMasker.

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL http://www.cecill.info.

As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability.

In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.

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