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I've written a paper about DNA sequence analysis. This paper attempts to use Bayesian modelling for a set of DNA sequences. It will probably end up either in a statistics journal, or, more likely, in a bioinformatics journal. My concern is that biologists may take exception to some of the language in the introduction.

I'm attempting to make a connection between De Novo motif discovery, and modelling the sequences. Maybe it is a bit of a stretch. E.g. I use language like "analyzing a set of DNA sequences with biological significance solely by focusing on the motifs contained within them potentially discards valuable information, for example, possible long-range correlations between nucleotide positions in the sequences." Also, "An alternative, and possibly complementary approach, is to consider a sequence as a single unit, and try to do direct statistical analysis on it... This approach is used in this paper, which does not use Markovian techniques. Instead, it tries to model correlation structure across the sequence."

So, the question is whether it is better to try to make an explicit connection at the risk of saying things that are incorrect and generally over-stretching, rather than just saying (which seems a little lame) that this sequence classification problem is related to De Novo motif discovery problem and leaving it at that. Comments?

I include the first few paragraphs of the introduction below. This includes all the relevant language.

I'm willing to send my current draft to anyone who is interested in knowing more about the context. I don't want to post a public link to it, though.

DNA sequence motifs are nucleotide sequence patterns that are conjectured to have a biological significance. Often they indicate sequence-specific binding sites for proteins such as nucleases and transcription factors (TF). Others are involved in important processes at the RNA level, including ribosome binding, mRNA processing (splicing, editing, polyadenylation) and transcription termination. Motif discovery is a very active area of research interest. So-called “De novo computational discovery” is perhaps the most popular, where given only a set of DNA sequences, an algorithm is used to identify candidate shared motifs. This can be thought of as the task of finding a set of non- overlapping, approximately matching substrings given a starting set of strings. This is a very difficult problem.

From a more general perspective, DNA sequence analysis is often done using DNA sequence motifs. It is reasonable to ask the question - what makes a sequence a motif? From a biological perspective, a motif is simply the smallest identifiable sequence sub- component of something larger. This subcomponent can be thought of as the smallest identifiable piece of functionality related to the underlying biology, Therefore, sequence analysis often focuses on identifying these motifs. However, these motifs are typically very short, so analyzing a set of DNA sequences with biological significance solely by focusing on the motifs contained within them potentially discards valuable information, for example, possible long-range correlelations between nucleotide positions in the sequences. Note also that the statistical methods used to identify motifs are typically Markovian, like Hidden Markov Models (HMM), which are naturally tailored towards looking at small sequences.

An alternative, and possibly complementary approach, is to consider a sequence as a single unit, and try to do direct statistical analysis on it. This approach is less often used. One reason is that such sequences can quickly grow too large, and are not well suited to Markovian approaches. This approach is used in this paper, which does not use Markovian techniques. Instead, it tries to model correlation structure across the sequence.

We do this by fitting a suitable Bayesian model to that set using Bayesian model selection. As noted above, our major rationale for this model is the assumption that the nucleotide locations of this set are correlated among themselves. With this assumption in mind, we construct a family of probability distributions to capture this correlation information, described in Subsection 2.1.

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I'm not technically a biologist, I'm a bioengineer, but even biologists understand the limitations of HMM for motif finding. If you can pick up on long-distance conserved disulfide bridges and that sort of thing, there's value in that. You haven't written anything that'll ruffle feathers that don't need a good ruffling. –  Jeremy Kemball Jun 19 at 22:35
    
@JeremyKemball Thanks for the feedback. Consider writing a formal answer, if you feel comfortable doing so. Not really sure what "disulfide bridges" are, though. –  Faheem Mitha Jun 19 at 22:53
    
Cysteine residues form -S-S- bonds across long sequence distances. They're a big structural/functional feature, one that's hard to detect with Markov models. So you're not implying anything too off-the-wall. I won't submit a formal answer, because I don't really work in this field. Maybe I'm missing something? Who knows. –  Jeremy Kemball Jun 19 at 23:25

1 Answer 1

Bioinformatics journals can deal perfectly with this type of papers. If you target a journal like Bioinformatics, then you can be as technical as you want (and you probably should). Biologists that read those journals will most likely understand the terminology.

Even traditional experimental biology journals, like Nucleic Acids Research, now include a section for Computational Biology that can be a perfect target for a paper on DNA motif analysis. If you submit to such a journal, however, you have to consider the target audience may be more broad than the typical Bioinformatics journal.

If you aim for Biologists to understand the concepts, you have to accept that there will be Biologists with very variable degrees of understanding of Bioinformatics. For example, as mentioned in some of the comments, some Biologists may understand what Hidden Markov Models are, others, however, may have never heard the term before. I would suggest that if you target a Biology centered journal, try to explain things in very simple terms, connecting the concepts to real life examples. You can use those explanations as introduction to more detailed descriptions. Depending on the journal, you may want to put the technical details, including formulas, in supplementary material. Keeping the technical details out of the main manuscript will make it accessible to general readership, yet having the details in supplementary material will give rigor to your paper and allow anyone interested in your research to check the details.

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Hi, I've read this a couple of times, but it does not appear to address my question. You seem to be answering a question I didn't ask, something like where is a good place to place such a paper. I'm asking a fairly specific question (perhaps not too well phrased), which could be summarized by the sentence "I'm attempting to make a connection between De Novo motif discovery, and modelling the sequences.". In a nutshell, I'm wondering if the statements I make in the intro (quoted) would be considered controversial or objectionable. –  Faheem Mitha Oct 6 at 9:06
    
Hi. Yes, it is possible that I did not understand your problem. I thought the quoted part was as an example of the type of description that you would put. My response was more in the line of how you should generally approach the writing to a Biologists oriented journal. If you are asking whether that specific piece of text should be clear enough to Biologists, then my opinion is that yes. For Biologists interested in transcription factors and other sequence related topics it should be easy to understand. –  ddiez Oct 6 at 9:21
    
Right. Well, my concern was not whether biologists would understand it (I think they would), so much as whether they would object to it. :-) –  Faheem Mitha Oct 6 at 13:13
    
Don't think they would object. I mean, the ones without much knowledge of the theory will appreciate the simplicity. The others, can check the more detailed descriptions. It also pretty much depends on who's your target audience! Maybe I should update my response with some of these thought? What do you think? –  ddiez Oct 6 at 13:39
    
Updating your answer sounds reasonable. Part of my question, implicitly, was whether my observations were conventional wisdom. See the comments on my question by Jeremy, which are pretty on target. –  Faheem Mitha Oct 6 at 16:38

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