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

From CCP4 wiki
(added my favorite tools -biased)
 
(Added further servers)
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*[http://nihserver.mbi.ucla.edu/SER/ Surface Entropy Reduction Prediction Server for making surface (lysine) mutations]
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====Characterisation====
*[http://www.strubi.ox.ac.uk/RONN RONN for identification of likely disordered regions]
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:* [http://www.sanger.ac.uk/Software/Pfam/ Pfam]
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:* [http://www.expasy.org/tools/protparam.html ExPASy ProtParam] Reports basic properties of a protein incl. reisdue composition, molecular weight, and predicted extinction coefficients.
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:* [http://smart.embl-heidelberg.de/ SMART] Domain Architecture
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:* [http://www.ch.embnet.org/index.html EMBNet Tools]
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:* [http://nihserver.mbi.ucla.edu/SER/ SERp] Surface Entropy Reduction Prediction Server for designing surface (lysine) mutations
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====Disorder prediction====
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:* [http://dis.embl.de/ DisEMBL 1.3] Predictors of protein disorder
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:* [http://bioinf.cs.ucl.ac.uk/disopred/disopred.html DISOPRED] Prediction of Protein Disorder Server
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:* [http://www.disprot.org/ DisProt] Database of Protein Disorder
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:* [http://bip.weizmann.ac.il/fldbin/findex FoldIndex]
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:* [http://globplot.embl.de/ GlobPlot 2.0] Predictor of disorder-globularity-domains
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:* [http://www.pondr.com/ PONDR] Predictor of Natural Disordered Regions
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:* [http://www.strubi.ox.ac.uk/RONN RONN (OPPF)]
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:* [http://www.bioinformatics.nl/~berndb/ronn.html RONN for multiple alignments]
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====Multiple Sequence Alignment====
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:* [http://www.ebi.ac.uk/clustalw/ Clustalw] General purpose multiple sequence alignment @ EBI
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:* [http://espript.ibcp.fr/ESPript/ESPript/ ESPript]  Generate "pretty" Postscript/PDF output from Multalin
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:* [http://xray.bmc.uu.se/dennis/ Indonesia] Java structure-based sequence alignment
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:* [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.
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:* [http://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.py MUSCLE] Multiple sequence comparison by log-expectation
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:* [http://timpani.genome.ad.jp/%7Emafft/server/ MAFFT] Multiple sequence alignment and NJ / UPGMA phylogeny
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:* [http://bioinfo.genopole-toulouse.prd.fr/multalin/multalin.html Multalin] Multiple sequence alignment with hierarchical clustering
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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

Revision as of 14:23, 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
  • 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