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 | ||
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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] | ||
:* [http://iupred.enzim.hu/ IUPRED] | |||
====Multiple Sequence Alignment==== | ====Multiple Sequence Alignment==== | ||
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:* [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 | ||
:* [http://ca.expasy.org/tools/scanprosite/ PROSITE] Motif Scan and alignment | |||
:* [http://www.bioinformatics.org/sms2/ident_sim.html SMS2] Calculate percentage sequence identity and similarity for aligned sequences | |||
====Other==== | |||
* [http://www.rostlab.org/services/CHOP CHOP] dissecting proteins into domain-like fragments based on sequence homology | |||
Latest revision as of 21:43, 30 July 2010
Characterisation[edit | edit source]
- 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 | edit source]
- OnD-CRF Predicting Protein Order and Disorder using Conditional Random Fields
- DisEMBL 1.3 Predictors of protein disorder
- DISOPRED Prediction of Protein Disorder Server
- DisProt Database of Protein Disorder
- FoldIndex
- GlobPlot 2.0 Predictor of disorder-globularity-domains
- PONDR Predictor of Natural Disordered Regions
- RONN (OPPF)
- RONN for multiple alignments
- IUPRED
Multiple Sequence Alignment[edit | edit source]
- 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 | edit source]
- CHOP dissecting proteins into domain-like fragments based on sequence homology