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Servers and programs for sequence analysis: Difference between revisions
Servers and programs for sequence analysis (edit)
Revision as of 15:23, 12 February 2008
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*[http://nihserver.mbi.ucla.edu/SER/ Surface Entropy Reduction Prediction Server for | ====Characterisation==== | ||
*[http://www.strubi.ox.ac.uk/RONN RONN for | :* [http://www.sanger.ac.uk/Software/Pfam/ Pfam] | ||
:* [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://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 | |||
====Disorder prediction==== | |||
:* [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://www.disprot.org/ DisProt] Database of Protein Disorder | |||
:* [http://bip.weizmann.ac.il/fldbin/findex FoldIndex] | |||
:* [http://globplot.embl.de/ GlobPlot 2.0] Predictor of disorder-globularity-domains | |||
:* [http://www.pondr.com/ PONDR] Predictor of Natural Disordered Regions | |||
:* [http://www.strubi.ox.ac.uk/RONN RONN (OPPF)] | |||
:* [http://www.bioinformatics.nl/~berndb/ronn.html RONN for multiple alignments] | |||
====Multiple Sequence Alignment==== | |||
:* [http://www.ebi.ac.uk/clustalw/ Clustalw] General purpose multiple sequence alignment @ EBI | |||
:* [http://espript.ibcp.fr/ESPript/ESPript/ ESPript] Generate "pretty" Postscript/PDF output from Multalin | |||
:* [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://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.py MUSCLE] Multiple sequence comparison by log-expectation | |||
:* [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://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 | |||