1,328
edits
Servers and programs for sequence analysis: Difference between revisions
Jump to navigation
Jump to search
→Disorder prediction: IUPRED
(added my favorite tools -biased) |
(→Disorder prediction: IUPRED) |
||
| (8 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
*[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://babel.ucmp.umu.se/fish/ FISH] Domain Family Identification using Structure-anchored HMMs | |||
:* [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://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://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] | |||
:* [http://iupred.enzim.hu/ IUPRED] | |||
====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://www.ebi.ac.uk/muscle/ MUSCLE] Multiple sequence comparison by log-expectation @ EBI | |||
:* [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://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 | |||