BE.180:Assignment1: Difference between revisions
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===Questions and Clarifications=== | ===Questions and Clarifications=== | ||
* Note that the stop codon TAA must be in frame, i.e. a multiple of 3 basepairs away from the ATG. For example, | * Note that the stop codon TAA must be in frame, i.e. a multiple of 3 basepairs away from the ATG. For example, ATGxxxxxxTAA would be in frame, but ATGxxxxxTAA would not be. (x is any basepair) | ||
* Is it significant that the barcode is CAPS and the other parts are lower case? | * Is it significant that the barcode is CAPS and the other parts are lower case? | ||
Revision as of 16:08, 16 February 2006
Assignment PDF
- Download Assignment 1 PDF
Parts
- Use this file as your input: Media:Parts.txt
Questions and Clarifications
- Note that the stop codon TAA must be in frame, i.e. a multiple of 3 basepairs away from the ATG. For example, ATGxxxxxxTAA would be in frame, but ATGxxxxxTAA would not be. (x is any basepair)
- Is it significant that the barcode is CAPS and the other parts are lower case?
- NO/no.
- Can an ORF be any length over 50, or should its length be a multiple of some small integer?
- An ORF should a length that is a multiple of three, the number of base pairs that comprise a codon
- Does the ORF include the start ATG and stop TAA? Suppose the DNA string is "ATG...TAA": is the ORF "..." or "ATG..." or "ATG...TAA" or "...TAA"?
- The ORF includes the "start" ATG and "stop" TAA.
- Can ORFs overlap? Suppose the DNA string is "ATG...TAAxxxTAA". The first ORF is obviously (modulo previous question) "ATG...TAA". Is "ATG...TAAxxxTAA" also an ORF? It meets the specification of "a string starting with ATG and ending with TAA". One could imagine a similar situation with overlapping starting tags: "ATG...ATGxxxTAA" might have both "ATG...ATGxxxTAA" and "ATGxxxTAA".
- Yes, ORFs can overlap.
