Servers and programs for sequence analysis

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  • Pfam
  • ExPASy ProtParam Reports basic properties of a protein incl. reisdue composition, molecular weight, and predicted extinction coefficients.
  • SMART Domain Architecture
  • EMBNet Tools
  • SERp Surface Entropy Reduction Prediction Server for designing surface (lysine) mutations

Disorder prediction

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