Posted 12 January 2005 - 10:34 PM
How do you guys predict the promoter sequence?
Posted 12 January 2005 - 11:19 PM
If it is human, you have pretty good chances to get the predicted promoter sequence from genome databases if there is no experimentally characterized promoter deposited in GenBank. You can go to ensembl.org to search for your gene and then export the 5'-flanking region which is highly likely the 5' regulatory region of your gene. The genome database has annotated human genome sequences using mulitple pipelines. Usually the prediction of 5'-flanking region or promoter is more accurate than stand-alone promoter prediction programs. For example, the pipelines align ESTs to genomic sequences. If a region aligns with many ESTs, this region may not be a non-coding seequence. Further, if this region is located immediately upstream a gene, most likely it is a promoter region. Because you wanna do methylation study on the promoter, the presence of CpG island is very important. After obtaining the sequence, analyze it for CpG islands, if there are, further suggesting the sequence Does contain a promoter.
Edited by pcrman, 12 January 2005 - 11:22 PM.
Posted 17 January 2005 - 08:48 AM
actually, i am working on rat genomes.