Name

gibbs

Program developed by Andrew Neuwald.

Web interface 1998 by

Description

The gibbs sampler detects motifs shared by a set of functionally related sequences.

Options

Input sequence:
The sequence that will be analyzed. Multiple sequences can be entered at once with most sequence formats (see below).

Format:
Input sequence format. Various standards are supported (click on the links for more details):

• raw: the raw sequence without any identifier or comment.
• multi: several raw sequences concatenated.
• IG: IntelliGenetics format.
• FastA: the sequence format used by FastA, BLAST, Gibbs sampler and a lot of other bioinformatic programs.
• Wconsensus: the format defined by Jerry Hertz for his programs (patser, consensus, wconsensus).

Sequence type
The program can analyse either proteic or DNA sequences.

Add reverse complement strand
For DNA sequences only, this option allows to detect motifs irrespective of the strand. The gibbs sampler does not include this option, we replace it by a trick consisting in analysing a modified sequence file including all the input sequences plus thir reverse complement.

Pattern length
This option determines the expected length for the motif. It is anessential parameter of the algorithm. Some patterns can be found with a specific length and missed with a different one.

Expected number of sites


This is the second essential parameter for the gibbs sampler. Fiddling around with this parameter will allow you to detect different patterns.

Availability

The gibbs sampler can be downloaded on Andrew Neuwald's ftp site (ftp://ncbi.nlm.nih.gov/pub/neuwald/) gibbs is writen in C and runs on unix machines (SUN, SGI have been tested). The web interface is a perl-cgi script.

Publications

• Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. & Wootton, J. C. (1993). Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262(5131), 208-14. PubMed ID 8211139
• Neuwald, A. F., Liu, J. S. & Lawrence, C. E. (1995). Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 4(8), 1618-32. PubMed ID 8520488