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

From CCP4 wiki
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:* [http://xray.bmc.uu.se/dennis/ Indonesia] Java structure-based sequence alignment
 
:* [http://xray.bmc.uu.se/dennis/ Indonesia] Java structure-based sequence alignment
 
:* [http://www.jalview.org/download.html Jalview] Java tool for MSA viewing, analysis and creation of publication-quality plots. Can run Clustalw, MAFFT and MUSCLE alignments.
 
:* [http://www.jalview.org/download.html Jalview] Java tool for MSA viewing, analysis and creation of publication-quality plots. Can run Clustalw, MAFFT and MUSCLE alignments.
:* [http://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.py MUSCLE] Multiple sequence comparison by log-expectation
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:* [http://www.ebi.ac.uk/muscle/ MUSCLE] Multiple sequence comparison by log-expectation @ EBI
 
:* [http://timpani.genome.ad.jp/%7Emafft/server/ MAFFT] Multiple sequence alignment and NJ / UPGMA phylogeny
 
:* [http://timpani.genome.ad.jp/%7Emafft/server/ MAFFT] Multiple sequence alignment and NJ / UPGMA phylogeny
 
:* [http://bioinfo.genopole-toulouse.prd.fr/multalin/multalin.html Multalin] Multiple sequence alignment with hierarchical clustering
 
:* [http://bioinfo.genopole-toulouse.prd.fr/multalin/multalin.html Multalin] Multiple sequence alignment with hierarchical clustering
 
:* [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

Revision as of 14:24, 12 February 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
  • Multalin Multiple sequence alignment with hierarchical clustering
  • Tcoffee A novel method for multiple sequence alignments. 3DCoffee mode performs structure-based sequence alignments