TE tools

Hadi Quesneville and I wrote a review article on “Discovering and detecting transposable elements in genome sequences” (Briefings in Bioinformatics 8:382-392) where we provide a table of links to transposable element (TE) bioinformatic tools. This page attempts to provide an up-to-date compendium of these and other TE-related bioinformatic resources. If you use this list of tools in a publication, please cite our original paper or this webpage. If you are aware of other relevant sites that are missing from this page, please let me know by email or post a comment below and I’ll be happy to add them to the list.

RESOURCE
LOCATION
AAARF https://sourceforge.net/projects/aaarf
ACLAME – A CLAssification of Mobile genetic Elements http://aclame.ulb.ac.be/
Alu Classifier http://clustbu.cc.emory.edu/calu/index.cgi
BLASTER suite http://urgi.versailles.inra.fr/index.php/urgi/Tools/BLASTER
BmTEdb http://gene.cqu.edu.cn/BmTEdb/
Censor http://www.girinst.org/censor/download.php
C-GATE https://sites.google.com/site/tecatalog/welcome
DAWG-PAWS http://dawgpaws.sourceforge.net/
DFAM http://dfam.janelia.org/
DomainOrganizer http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/DOMAIN/indexDOMAIN.php
dRIP http://dbrip.brocku.ca/searchRIP.html
DROPOSON ftp://biom3.univ-lyon1.fr//pub/drosoposon/
DyET http://www.pge.cnrs-gif.fr/pge/bioinfo/Dyet/
ELAN http://nldsps.jnu.ac.in/elan.html
find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl
FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm
FORrepeats http://al.jalix.org/FORRepeats/
Genome Artist http://www.genomeartist.ro
Greedier xli@cise.ufl.edu
Gypsy Database http://gydb.org/index.php/Main_Page
HelitronFinder http://limei.montclair.edu/HT.html
HomologMiner http://www.bx.psu.edu/miller_lab/
HelSearch http://sourceforge.net/projects/helsearch/files/
HERVd http://herv.img.cas.cz/
HMMER http://hmmer.janelia.org/
iMapper http://www.sanger.ac.uk/cgi-bin/teams/team113/imapper.cgi
IMDB – Insertional Mutagenesis DataBase http://imdb.nki.nl/
InFiRe http://www.infire.tu-bs.de/
Insertion Mapper http://sourceforge.net/projects/insertionmapper/
INTEGRALL http://integrall.bio.ua.pt/
IRF – Inverted Repeat Finder http://tandem.bu.edu/irf/irf.download.html
IScan http://www.ieu.uzh.ch/wagner/software/IScan/index.html
IS Finder http://www-is.biotoul.fr/is.html
ISsaga http://issaga.biotoul.fr/ISsaga/issaga_index.php
LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/
LTRdigest http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/ltrdigest.html
LTRharvest http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/ltrharvest.html
LTR_STRUC http://www.mcdonaldlab.biology.gatech.edu/ltr_struc.htm
LTR_MINER http://genomebiology.com/content/supplementary/gb-2004-5-10-r79-s5.pl
LTR_par http://www.eecs.wsu.edu/~ananth/software.htm
MAK http://wesslercluster.plantbio.uga.edu/mak06.html
MaskerAid http://blast.wustl.edu/maskeraid/
Maize Repeat database http://maize.jcvi.org/repeat_db.shtml
Maize TE database http://maizetedb.org/~maize/
MASiVE http://tools.bat.ina.certh.gr/masive/
MASiVEdb http://databases.bat.ina.certh.gr/masivedb/
McClintock https://github.com/bergmanlab/mcclintock
mer-engine http://roma.cshl.org/mer-source.php
MGEScan-LTR http://darwin.informatics.indiana.edu/cgi-bin/evolution/daphnia_ltr.pl
MGEScan-nonLTR http://darwin.informatics.indiana.edu/cgi-bin/evolution/nonltr/nonltr.pl
MIPS Repeat Element Database http://mips.helmholtz-muenchen.de/plant/siteUnderConstruction.jsp
microTranspoGene http://transpogene.tau.ac.il/microTranspoGene.html
Miropeats http://www.genome.ou.edu/miropeats.html
MITE-Hunter http://target.iplantcollaborative.org/mite_hunter.html
ModelInspector http://www.genomatix.de/online_help/help_fastm/modelinspector_help.html
ModuleOrganizer http://moduleorganizer.genouest.org
mreps http://bioinfo.lifl.fr/mreps/
mummer http://mummer.sourceforge.net/
MTID – Mouse Transposon Insertion Database http://mouse.ccgb.umn.edu/transposon/
MUST – MITE Uncovering SysTem http://csbl1.bmb.uga.edu/ffzhou/MUST/
ngs_te_mapper https://github.com/bergmanlab/ngs_te_mapper
OMWSA – Optimized Moving Window Spectral Analysis http://www.hy8.com/~tec/sw01/omwsa01.zip
PATIMDB http://ausubellab.mgh.harvard.edu/patimdb_application/
PBMice – PiggyBac Mutagenesis Info CEnter http://www.idmshanghai.cn/PBmice/index.jsp
P-Clouds http://www.evolutionarygenomics.com/PClouds.html
phiSITE http://www.phisite.org/
PILER http://www.drive5.com/piler/
PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl
Plant Repeat Database http://plantrepeats.plantbiology.msu.edu/
P-MITE http://pmite.hzau.edu.cn/django/mite/
Pneumococcal_repeat_annotation ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/
PoPoolationTE https://code.google.com/p/popoolationte/
process_hits http://sourceforge.net/projects/processhits/
Prophage Finder http://131.210.201.64/~phage/ProphageFinder.php
ProTIS http://www.cbs.umn.edu/labs/perry/Protocols/ProTIS.pl
Pseudomonas aeruginosa PA01 transposon database http://pseudomutant.pseudomonas.com/view.html
Pseudomonas aeruginosa PA14 transposon database http://ausubellab.mgh.harvard.edu/cgi-bin/pa14/home.cgi
RAP http://genomics.cribi.unipd.it/index.php/Rap_Repeat_Filter
RBR http://www.ii.uib.no/~ketil/bioinformatics/tools.html
REannotate http://www.bioinformatics.org/reannotate/index.html
ReAS ftp://ftp.genomics.org.cn/pub/ReAS/software/
RECON http://selab.janelia.org/recon.html
RelocaTE https://github.com/srobb1/RelocaTE
RepBase http://www.girinst.org/
RepClass http://sourceforge.net/projects/repclass/
RepeatExplorer http://galaxy.umbr.cas.cz:8080/
RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/
RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm
RepeatMasker http://www.repeatmasker.org/
RepeatModeler http://www.repeatmasker.org/RepeatModeler.html
RepeatRunner http://www.yandell-lab.org/software/repeatrunner.html
RepeatScout http://repeatscout.bioprojects.org/
repeat-match http://mummer.sourceforge.net/
REPET http://urgi.versailles.inra.fr/Tools/REPET
RepMiner http://repminer.sourceforge.net/index.htm
RepSeek http://wwwabi.snv.jussieu.fr/public/RepSeek/
REPuter http://bibiserv.techfak.uni-bielefeld.de/reputer/
ReRep http://bioinfo.pdtis.fiocruz.br/ReRep/
RetroBase http://biocadmin.otago.ac.nz/fmi/xsl/retrobase/home.xsl
RetroMap http://www.burchsite.com/bioi/RetroMapHome.html
RetroPred http://www.juit.ac.in/assets/RetroPred/home.html
RetroSearch http://www.daimi.au.dk/~biopv/herv/
RetroSeq https://github.com/tk2/RetroSeq
RetroTector http://www2.neuro.uu.se/fysiologi/jbgs/
RISCI – Repeat Induced Sequence Changes Identifier http://www.ccmb.res.in/rakeshmishra/tools/RISCI_Readme.htm
RJPrimers http://probes.pw.usda.gov/RJPrimers/index.html
RTAnalyzer http://www.riboclub.org/cgi-bin/RTAnalyzer/index.pl
RTCGD – Retrovirus Tagged Cancer Gene Database http://rtcgd.ncifcrf.gov/
RTClass1 http://www.girinst.org/RTphylogeny/RTclass1/
SAGRI – Spectrum Assisted Genomic Repeat Identifier http://sagri.comp.nus.edu.sg/
SeqGrapheR http://www.biomedcentral.com/imedia/6784621823926090/supp4.gz
SINE Base http://sines.eimb.ru/
SMaRTFinder http://services.appliedgenomics.org/software/smartfinder/
SoyTEdb http://www.soybase.org/soytedb/
Spanner https://github.com/chipstewart/Spanner
Spectral Repeat Finder http://www.imtech.res.in/raghava/srf/
STAN http://mobyle.genouest.org/cgi-bin/Mobyle/portal.py#forms::stan
Tallymer http://www.zbh.uni-hamburg.de/Tallymer/
TANGRAM https://github.com/jiantao/Tangram
TANTAN http://www.cbrc.jp/tantan/
TAPDANCE http://sourceforge.net/p/tapdancebio/home/Home/
TARGeT: Tree Analysis of Related Genes and Transposons http://target.iplantcollaborative.org/
TCF – Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html
TEA: TE Analyzer http://compbio.med.harvard.edu/Tea/
TEclass http://www.compgen.uni-muenster.de/tools/teclass/
TE Displayer http://labs.csb.utoronto.ca/yang/TE_Displayer/
TEfam http://tefam.biochem.vt.edu/tefam/
TE-locate http://sourceforge.net/projects/te-locate/
TEMP https://github.com/JialiUMassWengLab/TEMP
TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html
TESD – Transposable Element Simulator Dynamics http://pbil.univ-lyon1.fr/software/TESD/
TESeeker http://repository.library.nd.edu/view/16/index.html
TE-Tracker http://www.genoscope.cns.fr/TE-Tracker
TIF – Transposon Insertion Finder https://github.com/akiomiyao/tif
TINT – Transposition in Transposition http://www.bioinformatics.uni-muenster.de/tools/tint/
T-lex http://petrov.stanford.edu/cgi-bin/Tlex_manual.html
Tn Designation and Database Listing http://www.ucl.ac.uk/eastman/tn/
TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html
TranspoGene http://transpogene.tau.ac.il/
Transposon Express http://www.swan.ac.uk/genetics/dyson/TExpress_home.htm
Transposon Insertion Site Database http://transposon.abcc.ncifcrf.gov/
Transposon-PSI http://transposonpsi.sourceforge.net/
TRAP – Tandem Repeats Analysis Program http://www.coccidia.icb.usp.br/trap/tutorials/
TREP – Triticeae Repeat Sequence Database http://wheat.pw.usda.gov/ITMI/Repeats/index.shtml
TRF – Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html
TRIPLES – TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces http://ygac.med.yale.edu/triples/triples.htm
TROLL – Tandem Repeat Occurrence Locator http://finder.sourceforge.net/
TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/
Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm
Variation Hunter http://compbio.cs.sfu.ca/software-variation-hunter
VirusSeq http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html
VisualRepbase http://www.girinst.org/VisualRepbase/index.html
Vmatch http://www.vmatch.de/
WikiPoson http://www.bioinformatics.org/wikiposon/doku.php
WindowMasker http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/
WU-BLAST (now AB-BLAST) http://www.advbiocomp.com/blast.html

12 Comments

  1. Kamil Slowikowski

    Thanks for this excellent list!

  2. Excellent list of links! Very useful, thank you :)

  3. hongen
  4. Pablo
  5. Xudong Zhang

    Thanks you!
    FINDMITE,the website is not available.

  6. caseybergman

    Steve Moss has posted a nice tutorial on how to get ReAS running on OSX: http://stevemoss.posterous.com/compiling-reas-recovering-ancestral-transposa

  7. Alex Copeland

    Hi,

    Thanks for publishing this very useful list.

    I didn’t see SAGRI on your list.

    Spectrum-Based De Novo Repeat Detection in Genomic Sequences
    Huy Hoang Do, Kwok Pui Choi, Franco P. Preparata, Wing Kin Sung, Louxin Zhang.
    Journal of Computational Biology. June 2008, 15(5): 469-488. doi:10.1089/cmb.2008.0013.

    See http://www.liebertonline.com/doi/abs/10.1089/cmb.2008.0013#

    Best regards,
    Alex Copeland

  8. Dear Dr Bergman,

    Let me suggest you to add INTEGRALL, a curated integron database: http://integrall.bio.ua.pt/

    Best regards,
    Thomas Jové

  9. please add this database to the list. This database is a Bombyx mori Transposable Elements Database.

  10. zhenhui wang

    wonderful list! But i do not see any database of rice transposal elements, i want to know is there any of this information?Thank you!

  11. Douglas Hoen

    Great reference, thanks!

    FYI, the following links were broken when I tried them (suggested replacements in brackets, although I didn’t look for all of them).

    – IScan
    – LTR_STRUC (http://www.mcdonaldlab.biology.gatech.edu/ltr_struc.htm)
    – LTR_MINER (http://genomebiology.com/2004/5/10/R79/ or http://genomebiology.com/content/supplementary/gb-2004-5-10-r79-s5.pl)
    – mer-engine
    – Miropeats
    – RetroTector
    – RSPB
    – SAGRI
    – Transposon Express
    – Transposon Insertion Site Database
    – Variation Hunter (http://compbio.cs.sfu.ca/software-variation-hunter)

  12. caseybergman

    Many thanks Douglas, links are now edited or struckthrough where appropriate.


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