Protein Prediction
InterPro: InterProScan – InterPro
NCBI Conserved Domain Search: CD-Search: New Query
Biosequence analysis using profile hidden Markov Models: HMMER
Homology detection & structure prediction by HMM-HMM comparison/HHpred: Bioinformatics Toolkit
SMART: SMART: Main page
MOTIF: Searching Protein Sequence Motifs
AlphaFold Protein Structure Database: AlphaFold Protein Structure Database
3D structures from the Protein Data Bank (PDB): RCSB PDB: Homepage
TE annotation
TEtrimmer-2024: https://github.com/qjiangzhao/TEtrimmer
TransposonUltimate-2022: software for transposon classification, annotation and detection
Earl Grey-2024: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline
RepBox-2023: a toolbox for the identification of repetitive elements
IRF-2025-updated: Inverted Repeats Finder
gt-tirvish – Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.
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)
Database
tRNA database: http://gtrnadb.ucsc.edu/index.html
Rfam: https://rfam.org/
xfam:http://pfam-legacy.xfam.org/
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
DP-Bind: a web server for sequence-based prediction of DNA binding residues in DNA binding proteins
DNABIND: DNA Binding Protein prediction
TransBind TransBind Web Server
Protein-DNA binding specificity (TIR-DBD): DeepPBS
Expasy: Swiss Institute of Bioinformatics
STRING: a database of known and predicted protein-protein interactions
EVOLVE: Evolutionary Variation Observation Learning and Variant Exploration
ZnF-Prot: Zinc finger motifs in proteome
DNA binding site predictor for Cys2His2 Zinc Finger Proteins: Predicting DNA Recognition
HADDOCK2.4：https://wenmr.science.uu.nl/haddock2.4/
DNA and RNA fold
Internal Link
Storage: kodbox.mobilome.cn
Website: Mobilome Lab