To obtain transcription start site from a dna sequence
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4.0 years ago
bioinfo456 ▴ 150

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 • 999 views
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What is the organism your working on....??

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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.

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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?

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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.

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

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4.0 years ago

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.

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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.

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Not a problem at all, glad to help!