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find motives that might regulate genes

Given the complete sequence of an organismâ??s genome, 500 Mb, find motives that might regulate genes, based on the putative motivesâ?? proximity to known expressed genes. These motives are likely to occur relatively infrequently (ca. 1 motif/50 Kb).

Use the flow chart which I'm attaching because will help you, now answer the following questions with much details. Please you need only make as many notes as you can to each question. It's not important to be short and right answer, but try to make notice which help me to discuses my answers. I mean given answers and notices.

1.Restate the biological problem in computational terms. Be sure you understand any biological terms unfamiliar to you first.
2.What kinds of data do you need?
3.What controls do you need?
4.Do you need to define the problemâ??s conditions more precisely? How?
5.How would you represent the data and the problem?
6.Describe an algorithm for solving the problem.
7.How would you test the algorithmâ??s results? ( you do not have to answer it)

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Solution Preview

The information we are given is that the complete genome of this particular organism is 500 Mb (or, 500 million nucleotides per DNA strand). The problem is asking you to find potential regulatory motifs within the genome of this organism, based on the likelihood that such a motif would be found in proximity to known, expressed genes. Motifs control gene transcription (or regulation) through the interaction with transcription factors; basically, motifs are sequences within DNA which bind to transcription factors in a sequence-specific manner, and through this interaction genes are transcribed. Motifs are generally found in gene promoter regions, upstream from the transcription start site
Question 1: Biological terms to know are putative motifs, which are potential motifs that have not been identified as of yet but are strongly believed to be in a potential area within the genome. In this particular instance, the regulatory motifs are believed to be within the promoter ...

Solution Summary

This solution finds motives that might regulate genes, based on the putative motivesâ?? proximity to known expressed genes.