Promoter

Developed by Joe DeRisi, now at UCSF, Promoter is a package designed
to display features associated with genomes and to allow the user to perform
powerful searches to retrieve associated sequence data. This package is available
at both .. The display feature of Promoter is particularly relevant
because it creates genome maps with features annotated in genome order, and
with a correct scale representation of both the size and position of the feature on
the genome or chromosome of interest. Features are also correctly displayed on
either the Crick or Watson strands or can be marked as intergenic. By loading
an optional “gene data” fi le (consisting simply of a tab-delimited text fi le with
feature names and an associated log ratio, with each feature separated with a
carriage return), Promoter also has the ability to map onto the features data a
colorimetric representation of array data. Ultimately, Promoter produces output
in PostScript format suitable for direct importation in Adobe Illustrator or
similar vector-drawing software, where the annotation is then often customized
to suit the fi gure being created. An excerpt from a recently published example
is shown in Fig. 2, which illustrates the results for a single yeast chromosome
for a chromosomal immunoprecipitation array experiment performed using
antibodies against the Rap1 transcription factor (see Chapter 8 for a description
of chromosomal immunoprecipitation on chip methodology).
Although not a focus of this discussion, it should also be noted that Promoter’s
ability to extract primary sequence data from genetic regions corresponding
to hits in microarray experiments is an important preliminary step when
attempting to correlate array results with features of the primary sequence
data, such as when performing scans for the presence of possible regulatory
motifs. Promoter also has the ability to extract primary sequence-containing
motifs specifi ed by the user using the IUPAC degenerate nucleotide code, with
a user-selected acceptable number of mismatches from consensus.