From genomic position to predict protein binding

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Entering edit mode

9.2 years ago

sunearth • 0

I have a set of data which looks like this

chromosome    star           stop
chr1                3000122    300622
chr2                112233      113322
chr3                445566      455566

Basically, the data format looks like this. Is there anyway to predict possible protein binding to these regions?

CEAS needs WIG file which I don't have it. ( Can I generate it from what I have now?)

InterproScan keeps crash and took a long time to run just one fragment. I have 10 files and each file is 400MB.

Thanks

CNV BED protein-binding • 1.4k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 9.2 years ago by sunearth • 0

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Entering edit mode

That data format is essentially BED format, so if you had enough genomic intervals you could convert that into bedgraph (would need some score value).

As phrased, your question is extremely vague. Are you looking for transcription factor binding, or other factors? Are you trying to predict binding by motif content, or based on biological data such as ChIP experiments? If you clarify further, I'm sure you will get helpful and informative answers.

ADD REPLY • link updated 2.3 years ago by Ram 44k • written 9.2 years ago by Joseph Pearson ▴ 480

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