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TOOLS

Protein/Gene Homologue Detection

Jackhmmer — HMM-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

Secondary Structure Prediction

JPred — Secondary structure prediction server
PSIPRED — Secondary structure prediction server
RaptorX Property — Secondary structure, solvent accessibility, disorder prediction

Tertiary (3D) Structure Prediction

RaptorX — Template-based 3D structure prediction
I-TASSER — Template-based 3D structure and function prediction
EVfold — 3D structure prediction from evolutionary couplings

Evolutionarily-Coupled Residue-Residue Contact Prediction

RaptorX Contact Predict — Residue-residue contact prediction
PconsC3 — Residue-residue contact prediction
EVcouplings — Residue-residue contact prediction

Sequence Alignment

EMBOSS Needle — Align 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

Transmembrane Topology Prediction

TMHMM — Predict α-helical transmembrane segments in membrane proteins
OCTOPUS — Predict α-helical transmembrane segments in membrane proteins
MEMSAT — Predict α-helical transmembrane segments in membrane proteins
CCTOP — Predict α-helical transmembrane segments in membrane proteins

Domain and Motif Analysis

PROSITE — Searchable database of protein domains, families, and functional sites
SMART — Domain and motif detection tool

Signal Peptide Prediction

SignalP — Signal peptide prediction for proteins

Lipoprotein Prediction

LipoP — Lipoprotein prediction

Image Analysis & Cell Tracking Analysis Software

MicrobeJ — Microbial cell tracking and image analysis for microscopy movies
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