Hi, does anyone know where I can find a annotated database which specifically gives the genes and its promoters? I am new to bioinformatics and I need to analyse the promoters but I cant seem to find the right sources. Any suggestions will be much appreciated.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Here is a small set of tools for promoter analyses: http://molbiol-tools.ca/Promoters.htm
If you are only looking for databases then google is your friend. Here are a couple of examples: http://epd.vital-it.ch/ http://rulai.cshl.edu/CSHLmpd2/
-
Originally posted by Bioinformatic1 View PostHi, does anyone know where I can find a annotated database which specifically gives the genes and its promoters? I am new to bioinformatics and I need to analyse the promoters but I cant seem to find the right sources. Any suggestions will be much appreciated.
I don't think there is a clear understanding yet of what an eukariotic promoter exactly looks like and where it starts and finishes. Have a look at wikipedia http://en.wikipedia.org/wiki/Promoter_%28genetics%29 for a start.
Often genome-wide studies consider the "promoter" of a gene the region around the transcription start site. Typical regions are 100 or 1000 bp downstream and upstream the start site or 100bp downstream and 1000 bp upstream (since the promoter is expected to be upstream) or something on these lines. As I said, there is no clear cut definition as far as I know.
So your question could be reformulated as "Where do I get the position of the transcription start sites?" and the answer is UCSC genome browser or ensembl, if your species is there.
Hope this helps
Dario
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 08:47 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
Yesterday, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
54 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
Comment