Servers and programs for sequence analysis

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