User: guixien

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Posts by guixien

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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 11 days 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 12 days ago by guixien0 • updated 12 days ago by Mensur Dlakic1.7k
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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 8 months ago by guixien0

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