Questions tagged [transcription-factors]

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What's the meaning of Txn factor?

The transcription factor track in UCSC is named as Txn factor. Why Txn == Transcription?
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39 views

Is there a software that can predict protein-DNA binding?

Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
2
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0answers
43 views

Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?

I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
1
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2answers
381 views

Biological replicates on Chip-seq Transcription factor data

I have 2 biological replicates for chip-seq transcription factor data and I have applied macs2 peak calling for each replicate separately. How can i make use of the biological replicates to extract ...
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1answer
72 views

how to obtain GRCh38 bed and symbol files for HOCOMOCOv11

I am trying to a recently published software called diffTF and contacted the authors on how to obtain the input HOCOMOCO files for GRCh38. While I wait for the answer, I thought I would post the ...