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Protein/Gene Homologue Detection

JackhmmerHMM-based iterative search vs. protein sequence database
BLASTp — Sequence-based protein-protein database search
HHpred — HMM-based iterative search vs. protein sequence and/or structure database
KEGG — Sequence database for annotated genomes
JPredSecondary structure prediction server
PSIPREDSecondary structure prediction server
RaptorX PropertySecondary structure, solvent accessibility, disorder prediction
RaptorXTemplate-based 3D structure prediction
I-TASSERTemplate-based 3D structure and function prediction
EVfold3D structure prediction from evolutionary couplings
RaptorX Contact PredictResidue-residue contact prediction
PconsC3 Residue-residue contact prediction
EVcouplings Residue-residue contact prediction
EMBOSS NeedleAlign two protein or DNA sequences (pair-wise alignment)
Clustal Omega — Align three or more protein, DNA, or RNA sequences
T-COFFEE — Align three or more protein, DNA, or RNA sequences
MUSCLE — Align three or more protein or DNA sequences
TMHMMPredict α-helical transmembrane segments in membrane proteins
OCTOPUSPredict α-helical transmembrane segments in membrane proteins
MEMSATPredict α-helical transmembrane segments in membrane proteins
CCTOPPredict α-helical transmembrane segments in membrane proteins
PROSITESearchable database of protein domains, families, and functional sites
SMARTDomain and motif detection tool
SignalPSignal peptide prediction for proteins
LipoPLipoprotein prediction
MicrobeJMicrobial cell tracking and image analysis for microscopy movies
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