Servers and programs for sequence analysis: Difference between revisions

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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.
:* [http://www.expasy.org/tools/protparam.html ExPASy ProtParam] Reports basic properties of a protein incl. reisdue composition, molecular weight, and predicted extinction coefficients.
:* [http://smart.embl-heidelberg.de/ SMART] Domain Architecture
:* [http://smart.embl-heidelberg.de/ SMART] Domain Architecture
:* [http://babel.ucmp.umu.se/fish/ FISH] Domain Family Identification using Structure-anchored HMMs
:* [http://www.ch.embnet.org/index.html EMBNet Tools]
:* [http://www.ch.embnet.org/index.html EMBNet Tools]
:* [http://nihserver.mbi.ucla.edu/SER/ SERp] Surface Entropy Reduction Prediction Server for designing surface (lysine) mutations
:* [http://nihserver.mbi.ucla.edu/SER/ SERp] Surface Entropy Reduction Prediction Server for designing surface (lysine) mutations


====Disorder prediction====
====Disorder prediction====  
:* [http://babel.ucmp.umu.se/ond-crf/ OnD-CRF] Predicting Protein Order and Disorder using Conditional Random Fields
:* [http://dis.embl.de/ DisEMBL 1.3] Predictors of protein disorder
:* [http://dis.embl.de/ DisEMBL 1.3] Predictors of protein disorder
:* [http://bioinf.cs.ucl.ac.uk/disopred/disopred.html DISOPRED] Prediction of Protein Disorder Server
:* [http://bioinf.cs.ucl.ac.uk/disopred/disopred.html DISOPRED] Prediction of Protein Disorder Server

Revision as of 20:19, 5 May 2008

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

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
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