2008 post: On the promoter array analysis server

NimbleGen Promoter Arrays Mark Bieda server Analysis

Note: minor corrections on June 9, 2008
The promoter array server is located at this site

IMPORTANT USAGE NOTE: USE FIREFOX (Internet explorer appears to create issues)

What does it do?

1. This does a simple list comparison using NimbleGen .tab files
In other words, it just outputs the number of entries that are the same in the lists for the top100, top 200, etc.
2. this is a very simple application; just a convenience, really
3. this does not do an analysis like TAMALPAIS (see the category on TAMALPAIS on this blog).

File format:
this is based on the .tab file format from NimbleGen; it has to have a dummy line to begin.
here is a sample of an ok file format:

first dummy line
genenameholder CHR10_100017497_100020197 maxfourv02 0.2025
genenameholder CHR10_100164431_100167131 maxfourv02 0.7775
genenameholder CHR10_100196194_100198894 maxfourv02 0.6625

Notes on the format:
1. IMPORTANT: all fields are separated by tabs
2. The first field can vary and be meaningful.
3. The third field can vary and be meaningful.
4. The second field is the promoter name used for comparisons
5. The fourth field is the promoter value (numerical value) used for sorting (that is, determining order).
6. It’s ok to have more fields than the four. In other words, files of 10 fields are ok too. But the program will only look at the second and fourth fields.

Notes on usage:
1. the data can be entered unsorted

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