| Sequence Searching (Primary databases) | ||
|---|---|---|
| BLAST | http://www.ncbi.nlm.nih.gov/blast/ | Sequence database search at the NCBI |
| FASTA | http://www.ebi.ac.uk/fasta33/ | FASTA sequence database search |
| Motif Searching (Secondary databases) | ||
| InterPro | http://www.ebi.ac.uk/interpro | Integrated resource of secondary databases |
| PRINTS | http://umber.sbs.man.ac.uk/dbbrowser/fingerPRINTScan/ | PRINTS secondary database |
| BLOCKS | http://blocks.fhcrc.org/blocks_search.html | BLOCKS secondary database |
| ProSite | http://www.ebi.ac.uk/ppsearch/ | ProSite secondary database |
| Pfam | http://www.sanger.ac.uk/Software/Pfam/search.shtml | Pfam secondary database |
| MOTIF | http://motif.genome.jp/ | Integrated motif searching resource |
| DNA to Protein Translation | ||
| Expasy | http://www.expasy.ch/tools/dna.html | 6-frame translation software |
| Secondary Structure Prediction | ||
| JPRED | http://www.compbio.dundee.ac.uk/~www-jpred/ | Secondary structure prediction |
| GOR-III | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gib.html | GOR-III SS Prediction |
| GOR-IV | http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html | GOR-IV SS Prediction |
| GOR-V | http://gor.bb.iastate.edu/ | GOR-V SS Prediction |
| PSIPred | http://www.psipred.net/ | PSIPred SS Prediction - probably the best! |
| Transmembrane Prediction | ||
| TSEG | http://www.genome.ad.jp/tools/tseg/ | Predict membrane proteins |
| TMHMM-2.0 | http://www.cbs.dtu.dk/services/TMHMM-2.0/ | TM prediction through Hidden Markov Models |
| TopPred | http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html | Predict location and orientation of transmembrane helices through an advanced use of hydrophobicity patterns, and by applying the 'positive-inside' rule |
| DAS | http://www.sbc.su.se/~miklos/DAS/ | TM Prediction through an advanced use of hydrophobicity patterns |
| MemSat | http://www.psipred.net/ | MemSat TM prediction (on the same page as PsiPred) |
| Post-translational Modification Prediction | ||
| NetPhos | http://www.cbs.dtu.dk/services/NetPhos/ | NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences. |
| NetOGlyc | http://www.cbs.dtu.dk/services/NetOGlyc/ | The NetOglyc WWW server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. |
| big-PI | http://mendel.imp.univie.ac.at/gpi/gpi_server.html | GPI Modification Site Prediction |
| Threading and Fold Recognition | ||
| SAM-T06 | http://www.soe.ucsc.edu/research/compbio/SAM_T06/T06-query.html | An HMM based method to find remote homologs. |
| phyre | http://www.sbg.bio.ic.ac.uk/~phyre/ | Fold recognition (Protein Homology/analogY Recognition Engine) |
| GenThreader | http://www.psipred.net/ | Fast threading - on the same site as PSIPred |
| Comparative Modelling Servers | ||
| Swiss-Model | http://www.expasy.ch/swissmod/SWISS-MODEL.html | An Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland |
| CPHmodels | http://www.cbs.dtu.dk/services/CPHmodels/ | A neural net based comparative modelling tool |
| CYSPRED | http://gpcr.biocomp.unibo.it/cgi/predictors/cyspred/pred_cyspredcgi.cgi | Disulphide prediction |
| Sequence Alignment | ||
| ClustalW | http://www.ebi.ac.uk/clustalw/ | Multiple sequence alignment at the EBI. |
| ClustalW | http://www.ch.embnet.org/software/ClustalW.html | |
| Sequence-based Profiles | ||
| ProtScale | http://www.expasy.ch/cgi-bin/protscale.pl | Plot various sequence-based profiles (hydrophobicity, secondary structure, etc.) |
| Signal-Peptide Prediction | ||
| PSORT | http://psort.ims.u-tokyo.ac.jp/ | Predict protein sorting signals |
| SignalP | http://www.cbs.dtu.dk/services/SignalP/ | Signal peptides |
| Integrated Prediction Systems | ||
| PredictProtein | http://www.predictprotein.org | Prediction system from Columbia University (also available at The EBI) Includes PHD secondary structure prediction, ProSite, domain prediction, threading, solvent accessibility, TM, etc. |
I have completed this work to the best of my ability.