Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

GibbsCluster-1.1 Server

Simultaneous alignment and clustering of peptide data

Update (Dec 2015): New fast version of the algorithm (1.1). It can improve speed by up to 10-fold on large data sets with minor impact on predictive performance. To retain the behaviour of the 1.0 version, untick the "Fast mode" option.

NOTE. If your data set is large (>1000 sequences) and the execution is expected to be longer than 10 hours, please use this version of the server GibbsCluster Heavy Queue or DOWNLOAD a stand-alone version to install on your system.

Instructions Output format Data sets Article abstract Downloads

DATA SUBMISSION

Paste peptides in the box:

or submit a file directly from your local disk:



Sample data: Sample 1 - Sample 2

SUBMIT job



Optionally set some of the parameters before starting your job


BASIC options

Hover the mouse cursor over the symbol for a short description of the options

Perform alignment?
YES NO

Number of clusters

Motif length


ADVANCED options

Number of seeds for initial conditions

Penalty factor for inter-cluster similarity (λ)

Weigth on small clusters (σ)

Use trash cluster to remove outliers


VERY ADVANCED options

Number of iterations per sequence per temperature step

Initial Monte Carlo temperature

Number of temperature steps

Interval between Single Peptide moves

Interval between Phase Shift moves

Background amino acid frequencies

Preference for hydrophobic AAs at P1

Blosum matrix

Sequence weighting type

Fast mode (recommended for large datasets)

Prefix to result files



SUBMIT job



Confidentiality:
The sequences are kept confidential and will be deleted after processing.


CITATIONS

For publication of results, please cite:

    Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
    Andreatta M, Lund O, Nielsen M
    Bioinformatics (2012) doi: 10.1093/bioinformatics/bts621
    Abstract


PORTABLE VERSION

Would you prefer to run GibbsCluster locally? A portable version for the most common UNIX platforms is available at this download page for academic users. Other users are requested to contact CBS Software Package Manager at software@cbs.dtu.dk.


GETTING HELP

Scientific problems:        Technical problems: