TE annotation
Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection
TransposonUltimate-2022: software for transposon classification, annotation and detection
Earl Grey-2024: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline
Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes
Transposable Element Finder – Detection of active transposable elements from NGS data
Transposome-2015: a toolkit for annotation of transposable element families from unassembled sequence reads
RepeatFiller-2019: newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements
reputils: A small collection of command line functions to deal with TE alignments.
repeatR: read and analyse RepeatMasker output
RepBox-2023: a toolbox for the identification of repetitive elements
TARGeT: Tree Analysis of Related Genes and Transposons
TIR detection
IRF-2025-updated: Inverted Repeats Finder
MUSTv2-2017: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs)
MiteFinderII-2018: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes
MITE Tracker-2018: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
IUPACpal-2021: efficient identification of inverted repeats in IUPAC-encoded DNA sequences
detectIR-2016-updated: detectIR download | SourceForge.net
gt-tirvish – Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.
Lirex-2017: A Package for Identification of Long Inverted Repeats in Genomes
detectMITE-2016: A novel approach to detect miniature inverted repeat transposable elements in genomes
MITE-Hunter-2010: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
MITE Digger-2013, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements
TIRfinder-2013: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats
TIR-Learner: Modified TIR-Learner for Rice genome
TIR-Learner v3: New generation TE annotation program for identifying TIRs
TSDfinder: The TSDfinder tool identifies TSDs plus non-LTR retrotransposon-driven transductions.
Gene/ORF and domain Prediction
Promoter: https://molbiol-tools.ca/Promoters.htm
GeneMark (Prokaryotic ): GeneMark gene prediction (gatech.edu)
Prodigal (Prokaryotic): Fast, reliable protein-coding gene prediction for prokaryotic genomes
Genscan: New GENSCAN Web Server at MIT
GetORF: EMBOSS: getorf (bioinformatics.nl)
ORFfinder: ORFfinder Home – NCBI (nih.gov)
Genome tool
tRNA database: http://gtrnadb.ucsc.edu/index.html
Rfam: https://rfam.org/
xfam:http://pfam-legacy.xfam.org/
InterPro:https://www.ebi.ac.uk/interpro/
Ensemble: https://www.ensembl.org/index.html
Animal Genome Size: Animal Genome Size Database:: Home
Genome browse: https://www.ncbi.nlm.nih.gov/genome/browse
Galaxy: https://usegalaxy.org/?msclkid=038ffcd4b64211eca081527e1ddb66da
BARCH ENTREZ: https://www.ncbi.nlm.nih.gov/sites/batchentrez
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
EMBOSS: http://www.bioinformatics.nl/emboss-explorer/
CD-HIT: http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi
USEARCH： https://drive5.com/
SeqLogo: http://weblogo.berkeley.edu/logo.cgi
Tree
TimeTree: http://www.timetree.org/
TolTree: http://tolweb.org/tree/
Lifemap: http://lifemap-ncbi.univ-lyon1.fr/
RNA
RNA-Protein Interaction Prediction (RPISeq)
omiXcore: a web server for prediction of protein interactions with large RNA
Protein tools and server
*DNA binding motif prediction: https://predictprotein.org/
GraphSite: AlphaFold2-aware protein-DNA binding site prediction using graph transformer
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins.
DNABIND: DNA Binding Protein prediction
MOTIF: https://www.genome.jp/tools/motif/
ZnF-Prot: Zinc finger motifs in proteome
DNA binding site predictor for Cys2His2 Zinc Finger Proteins: Predicting DNA Recognition
Transposase domains prediction: NCBI Conserved Domain Search (nih.gov)
HMMsearch: https://www.ebi.ac.uk/Tools/hmmer//search/phmmer
Alphafold: https://alphafold.ebi.ac.uk/search/organismScientificName/Escherichia%20coli%20%28strain%20K12%29
HADDOCK2.4：https://wenmr.science.uu.nl/haddock2.4/
DNA and RNA fold
Internal Link
Storage: kodbox.mobilome.cn
Website: Mobilome Lab