Difference between revisions of "Servers and programs for sequence analysis"

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:* [http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi Tcoffee] A novel method for multiple sequence alignments. 3DCoffee mode performs structure-based sequence alignments
 
:* [http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi Tcoffee] A novel method for multiple sequence alignments. 3DCoffee mode performs structure-based sequence alignments
 
:* [http://ca.expasy.org/tools/scanprosite/ PROSITE] Motif Scan and alignment
 
:* [http://ca.expasy.org/tools/scanprosite/ PROSITE] Motif Scan and alignment
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:* [http://www.bioinformatics.org/sms2/ident_sim.html SMS2] Calculate percentage sequence identity and similarity for aligned sequences

Revision as of 00:24, 9 March 2008

Characterisation

  • 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