Biostar Beta. Not for public use.
To obtain transcription start site from a dna sequence
0
Entering edit mode
12 months ago
Indian Institute of Technology, Madras,…

I have a number of DNA sequences. Each sequence is either up or downstream of an SNP. How can I compute the presence of transcription start site from it? Thanks for your insight.

dna sequence • 402 views
ADD COMMENTlink
0
Entering edit mode

What is the organism your working on....??

ADD REPLYlink
0
Entering edit mode

compute the presence of transcription start site

Welcome to biology, where we do appropriate experiments to deduce features like this, and where not everything can simply be computed.

ADD REPLYlink
0
Entering edit mode

Experimentally speaking, can I use an already identified dataset of TSS containing its locations and accordingly check if it falls within the range of my dna sequences?

ADD REPLYlink
1
Entering edit mode

Yes - but ideally you would use TSS determined in your tissue of interest as this level of regulation can be dependent on the cell type.

ADD REPLYlink
0
Entering edit mode

I'm interested in the brain tissues. Which folder here contains that information?

ADD REPLYlink
1
Entering edit mode
14 months ago
Seattle, WA USA

You could map your sequences to a model genome assembly (e.g., hg38 for human genome, etc.) with a tool like Bowtie2, which recovers intervals where those sequences map, and associate them with genomic annotations like Gencode, Ensembl, CAGE, etc. using a tool like BEDOPS bedmap, which can give you strand and offsets from which to derive the position of the TSS within the original input sequence.

ADD COMMENTlink
0
Entering edit mode

Thanks for insisting on BEDOPS. The sequences I have are a result of mapping with hg38. I'm having a hard time finding the TSS determined in cerebellum, prefrontal cortex, temporal cortex tissues. Would appreciate if you could help me with that.

ADD REPLYlink
0
Entering edit mode

Not a problem at all, glad to help!

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1