Promolign is a tool for graphical presentation of
SNPs and
transcription factor binding sites at
promoter region of genes in the context of human-mouse
orthologous sequence alignment.
It is developed for CREATE network
(Comprehensive Research on Expressed Alleles in Therapeutic Evaluation) coordinated by
Dr. Howard McLeod
in Washington University in St. Louis, who is a member of
Pharmacogenetics Research Network.
It is implemented by
Tao Zhao in the laboratory of
Dr. Gary Stormo.
The Human-mouse ortholog genes are
from
MGI Mammalian Orthology and Comparative Maps.
The promoter region is defined as 10kb sequence
upstream of TSS (transcription start site).
The annotation and sequence of this region are from
NCBI Map Viewer
(human genome build 33, mouse genome build 30). Biweekly update is planned to accomodate
any occational change to major NCBI genome build.
The repetitive elements and low complexity fragments are masked with
RepeatMasker.
The human and mouse sequences are aligned with
WU-BLAST2.0
with optimization for human-mouse homology alignment.
The transcription factor binding sites are denoted with
TRANSFAC.
SNPs are collected from various sources, including
dbSNP,
CGAP,
JSNP,
as well as resequencing project of CREATE network.
All the information is stored in a
mySQL
database.
Promolign initially contained
126 genes that are involed in several
cancer drug pathways
in CREATE
network research project. It has since been upgraded to genomic level with
more than 6,000 human-mouse orthologous gene pairs in its
database.
Promolign graphics are rendered with SVG
(Scalable Vector Graphics).
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© CREATE network, Washington University in Saint Louis.
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