Binding site predictions and (new) basic localization analysis and gene identification
for ChIP-chip experiments using NimbleGen tiling arrays. Originally designed for arrays with 350,000 - 400,000 oligos but may be used in other designs.These arrays should be relatively high density (i.e., < 100 bp spacing), as in ENCODE arrays. Contact Mark Bieda
if you have questions. Do not
use this for promoter arrays.
The statistical model and methodology used by the TAMALPAIS server is described in Bieda et al., 2006 Genome Research 16:595. Available here
. The complete package of software (for Linux only) is available from Mark Bieda
. For more information: Why use Tamalpais? And other Methods Information
To access sample data, go to Sample Data Download PagePlease reference Bieda et al., 2006 Genome Research 16:595 if you use results from this website!
1. Specify 1-3 gff files containing NimbleGen array data ('ratio' files).
These files may be submitted as "raw" gff files or compressed ".zip" files. For compressed files, submit a separate zip for each gff file (to do this: Windows and Mac OS use default compression; for linux use zip not gzip)
Important Note on Data Privacy: We will not use your data in any way unless your file generates errors, and you will be informed of this in the rare event that it happens.