Can HMMs detect partial proteins sequences?
I am trying to determine the abundance of a gene in a set of metagenomic short reads using the hmm of this gene, then use this method to compare the abundance of the gene across several samples after normalizing for data size. What I would do is to first translate the genes into ORFs, then run hmm against the reads. Since the amino acid sequence of this HMM is longer (~220 amino acids) than the read length (150 bases, which translates to ~50 amino acids), I am wondering if hmm can accurately detect the partial sequences and still report hits?
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