Generate DNA string

Question

[فاطمه]

Q1/we need to ensure that a motif with the same or even larger score is unlikely to occur in a collection of "typical" DNA strings (of the same length).

How would you generate these strings? Q2/When using motif software with fixed motif lengths, is it better to start with short motifs or long motifs? Why?

[Hamid Ghaedi]

To make sure that your question will get an answer, provide as much as possible information and context on the topic.Also using appropriate and more specific tag (like name for the software instead of "software" term) would direct your question to the attention of right people with knowledge in the field. That being said , your question looks like a homework which is not necessarily inappropriate to ask for answer, but people would like to answer this kind of question when they could see what you have tried so far.So do not hesitate to modify the post to make it sound more specific and also share your code.

Answer 1

[Alex Reynolds]

How would you generate these strings?

You might start with thinking about what typical DNA strings might look like, if you were to generate a set of strings at random.

For example, the simplest model might look like a 1/4 probability of seeing each base at a given position of a motif. To generate a random sequence of length n, roll a fair four-sided die n times, etc.

Using this model to generate a set of randomly generated strings, you might ask how often you expect to see your motif by chance, based on the frequency of strings you'd expect to generate.

In reality, the underlying biology shows dependencies between bases in areas of the genome where transcription factors bind, such as promoters. So more complicated models like, say, heximer frequency or GC content can be used to generate a more biologically relevant background set of sequences.

[seidel]

If you found your motif based on some set of strings from an experiment, you could also try (1) scrambling them (i.e. shuffling the order of the bases of all the strings), (2) taking some DNA regions adjacent to the strings you used, (3) generate random strings using the base frequencies of your original set (sort of what Alex suggest in the last sentence of his answer).