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

From CCP4 wiki
(Added further servers)
(Disorder prediction: IUPRED)
 
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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
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:* [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====
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====Disorder prediction====  
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:* [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
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:* [http://www.strubi.ox.ac.uk/RONN RONN (OPPF)]
 
:* [http://www.strubi.ox.ac.uk/RONN RONN (OPPF)]
 
:* [http://www.bioinformatics.nl/~berndb/ronn.html RONN for multiple alignments]
 
:* [http://www.bioinformatics.nl/~berndb/ronn.html RONN for multiple alignments]
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:* [http://iupred.enzim.hu/ IUPRED]
  
 
====Multiple Sequence Alignment====
 
====Multiple Sequence Alignment====
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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
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:* [http://www.ebi.ac.uk/mafft/ MAFFT] Multiple sequence alignment and NJ / UPGMA phylogeny @ EBI
 
:* [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
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:* [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
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====Other====
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* [http://www.rostlab.org/services/CHOP CHOP] dissecting proteins into domain-like fragments based on sequence homology

Latest revision as of 20:43, 30 July 2010

Characterisation[edit]

  • 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[edit]

Multiple Sequence Alignment[edit]

  • 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

Other[edit]

  • CHOP dissecting proteins into domain-like fragments based on sequence homology