Please enter your protein or DNA sequence(s) in fasta format (make sure you have a newline between the fasta-header and the sequence!). Note: you can now enter multiple sequences!

Alternatively (or additionally), enter one or more genbank nucleotide accession numbers and all analyses will be done on the protein sequence found.
(Note: you are recommended NOT to use viral accession numbers!)

Please select the output type you would like displayed:

full
diagram only

Choose which programs you want to run on your sequence(s):

Base content (fasta-format DNA sequences only!)
Codon Usage (fasta-format DNA sequences only!)

Protein Calculator (sequence statistics)

SignalP (prediction of signal peptides)
TargetP (cellular location)
The signal sequence predictors need to know a bit about the host organsim:
     eukaryote
     gram positive bacteria
     gram negative bacteria

NetNGlyc (prediction of N glycosylation)
NetOGlyc (prediction of O glycosylation)
TMHMM (transmembrane prediction)
Predator (secondary structure prediction)

Blast the Conserved Domain Database (prediction of domain matches)
Blast SCOP (prediction of structural domains)
PDB Blast (finds nearest matches in the PDB)
TargetDB Blast (finds nearest matches in TargetDB)
MGC Clone Blast (finds nearest matches in MGC collection)
SwissProt Blast (finds nearest match in SwissProt)

Genbank nr Blast (finds nearest match in genbank's nr database - use this on it's own)
[ Please note that all Blast searches have the low complexity filter turned on. ]

Trypsin Cleavage (prediction of trypsin cleavage sites - class 1: fastest cleavage rates, class 4: slowest cleavage rates)
     class 1 only
     classes 1 and 2
     classes 1, 2 and 3
     all classes
[ For cleavage by other enzymes the PeptideCutter tool is recommended. ]

Calculate extinction coefficient at 280nm for constucts (based on protein calculator)
     pDEST17 tag
     pDESTH6N15 tag
     3C Cleavage tag

For disorder prediction, please use RONN

Other useful tools may be found on the ExPASy website and in the EBI Toolbox.

Useful protein interaction databases are DIP and BIND.

A new protein database: Human Protein Reference Database.

A good RNA secondary structure prediction program is mfold which you can download and run locally.

References:

Predator and all the Blast searches are done using local versions of the programs.
The PDB, conserved domain and TargetDB databases are updated as soon as new versions are available.

Predator:
Dmitrij Frishman
Deputy director
Institute for Bioinformatics
German National Center for Health and Environment
d.frishman@gsf.de
Dmitrij Frishman, the author of predator also has a web page.

Frishman,D & Argos,P.(1996) Incorporation of long-distance interactions into a secondary structure prediction algorithm. Protein Engineering, 9, 133-142.
Frishman, D. & Argos,P.(1997) 75% accuracy in protein secondary structure prediction. Proteins, 27, 329-335.

Protein Calculator: http://www.scripps.edu/~cdputnam/protcalc2.html
Christopher Putnam, Ph.D.
Ludwig Institute For Cancer Research
cdputnam@ucsd.edu

Trypsin Cleavage:
Tool developed by Rebecca Thomson, rebecca@strubi.ox.ac.uk
Based on data from Keil, B.(1992) Specificity of proteolysis. Springer-Verlag Berlin-Heidelberg-NewYork, pp.335.

Blast programs are available at: http://www.ncbi.nlm.nih.gov/BLAST

TargetDB is available to Blast search at http://www.ebi.ac.uk/msd/MSDServices/SGtargets.html

The other programs are run directly from the Center for Biological Sequence Analysis web server at the following URLs:
TMHMM http://www.cbs.dtu.dk/services/TMHMM
SignalP http://www.cbs.dtu.dk/services/SignalP
TargetP http://www.cbs.dtu.dk/services/TargetP
NetNGlyc http://www.cbs.dtu.dk/services/NetNGlyc
NetOGlyc http://www.cbs.dtu.dk/services/NetOGlyc

Other servers used:
PSORT http://psort.nibb.ac.jp/
SCOP - ANDOM http://www.bork.embl-heidelberg.de/AnDom/