User: guixien

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Posts by guixien

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Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)
... Suppose I have done two Chip-seq experiments. Now after the bias correction step such as MACS2, I get two set of genomic intervals (or peaks, as what is usually called) that corresponds to each of the experiment. I want to test the significance of the overlap of two genomic intervals. The common te ...
hypergeometic test chip-seq statistics written 12 weeks ago by guixien0
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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), instead of using Baum Welch. I suspect that this is the case because this is what I saw in the current ve ...
hmm motif hidden markov model transcription factor written 9 months ago by guixien0
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Comment: C: What's the point in estimating the background distribution in probabilstic model
... Yes. I am guessing that's the reason why HMMER3 does not include a Baum-Welch training procedure to train a profile HMM, since eventually the estimated background distribution during the training is going to be "discarded" anyway when performing a homology search in a database? ...
written 10 months ago by guixien0
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What's the point in estimating the background distribution in probabilstic models of motif finding such as MEME (mixture model with EM) or some HMM?
... I suppose that in the database searching for homologous sequence using the profiles created by whether MEME (represented by a PWM) or a HMM (represented by some profile HMM) make use of the log odds ratio with the random model being an independent process with the emission probability being the disc ...
motif sequence homology sequence analysis written 10 months ago by guixien0 • updated 10 months ago by Mensur Dlakic6.0k
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MEME-chip: selecting the input sequences to be equal length
... So after executing the peak calling program like MACS2, I get the bed file with peak intervals of different length. Now my question is: what are some of the common steps to select the top sequences and set them to equal length before using MEME-chip? Are there any statistical justifications behind i ...
meme-chip meme x-seq chip-seq written 18 months ago by guixien0

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