Servers and programs for sequence analysis
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Characterisation
- Pfam
- ExPASy ProtParam Reports basic properties of a protein incl. reisdue composition, molecular weight, and predicted extinction coefficients.
- SMART Domain Architecture
- FISH Domain Family Identification using Structure-anchored HMMs
- EMBNet Tools
- SERp Surface Entropy Reduction Prediction Server for designing surface (lysine) mutations
Disorder prediction
- OnD-CRF Predicting Protein Order and Disorder using Conditional Random Fields
- DisEMBL 1.3 Predictors of protein disorder
- DISOPRED Prediction of Protein Disorder Server
- DisProt Database of Protein Disorder
- FoldIndex
- GlobPlot 2.0 Predictor of disorder-globularity-domains
- PONDR Predictor of Natural Disordered Regions
- RONN (OPPF)
- RONN for multiple alignments
Multiple Sequence Alignment
- Clustalw General purpose multiple sequence alignment @ EBI
- ESPript Generate "pretty" Postscript/PDF output from Multalin
- Indonesia Java structure-based sequence alignment
- Jalview Java tool for MSA viewing, analysis and creation of publication-quality plots. Can run Clustalw, MAFFT and MUSCLE alignments.
- MUSCLE Multiple sequence comparison by log-expectation @ EBI
- MAFFT Multiple sequence alignment and NJ / UPGMA phylogeny @ EBI
- Multalin Multiple sequence alignment with hierarchical clustering
- Tcoffee A novel method for multiple sequence alignments. 3DCoffee mode performs structure-based sequence alignments
- PROSITE Motif Scan and alignment
- SMS2 Calculate percentage sequence identity and similarity for aligned sequences
Other
- CHOP dissecting proteins into domain-like fragments based on sequence homology