|
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/ |
| INTEGRALL |
http://integrall.bio.ua.pt/ |
| IRF – Inverted Repeat Finder |
http://tandem.bu.edu/irf/irf.download.html |
| IScan |
http://www.bioc.uzh.ch/wagner/software/IScan/ |
| 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/finalLTR.htm |
| LTR_MINER |
http://genomebiology.com/2004/5/10/R79/suppl/s7 |
| 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/ |
| 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/ |
| 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/ |
| Pneumococcal_repeat_annotation |
ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/ |
| 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 |
| 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://www.kvir.uu.se/RetroTector/RetroTectorProject.html |
| 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/ |
| 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/ |
| TEA: TE Analyzer |
http://compbio.med.harvard.edu/Tea/ |
| TCF – Transposon Cluster Finder |
http://www.mssm.edu/labs/warbup01/paper/files.html |
| 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 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 |
| 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/strvar.htm |
| 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 |
Thanks for this excellent list!
Excellent list of links! Very useful, thank you
LTR_STRUC new website：
http://www.mcdonaldlab.biology.gatech.edu/finalLTR.htm
SMaRTFinder new site:
http://services.appliedgenomics.org/software/smartfinder/
Thanks you!
FINDMITE,the website is not available.
Steve Moss has posted a nice tutorial on how to get ReAS running on OSX: http://stevemoss.posterous.com/compiling-reas-recovering-ancestral-transposa
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
Dear Dr Bergman,
Let me suggest you to add INTEGRALL, a curated integron database: http://integrall.bio.ua.pt/
Best regards,
Thomas Jové
please add this database to the list. This database is a Bombyx mori Transposable Elements Database.
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!