Difference between revisions of "General Questions"
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A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring. <br> | A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring. <br> | ||
| + | |||
| + | ''Alternative ORFs''' <br> | ||
| + | Q: What if there's a possible Shine-Dalgarno sequence and start codon on the opposing strand in the middle of the gene you're working on? Do you assume that the computer has already marked it as a possible gene or do youhave to examine it as well? <br> | ||
| + | |||
| + | A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring. <br> | ||
| + | <br> | ||
| + | |||
| + | Q: How do we rate our judgment calls? Can we indicate confidence levels?<br> | ||
| + | |||
| + | A:Confidence levels (listed low to high) | ||
| + | #'''Hypothetical protein''': choose if selected "hypothetical protein" under "gene product"<br> | ||
| + | #'''Conserved hypothetical protein''': choose if selected "conserved hypothetical protein" under "gene product"<br> | ||
| + | *Not enough info to select "Family Membership" or "Function unclear" | ||
| + | *no domains identified | ||
| + | *no family membership)<br> | ||
| + | #'''Family membership''': Choose if conserved hypothetical protein identified via PFam or TIGRfam as belonging to a protein family but function and specificity are unclear.<br> | ||
| + | #'''Function unclear''': Choose if | ||
| + | *protein domain is identified | ||
| + | *protein function is unclear | ||
| + | *if "putative" or "possible" or "predicted" occur in all the significant Tigrfam, COG, or PFAM names<br> | ||
| + | #'''Specificity unclear''': Choose if only more general information on the function of a protein family is available | ||
| + | E.g., ABC transporter (but can't predict substrate) | ||
| + | E.g., Histidine kinase (but can't predict target response regulator) | ||
| + | High confidence in function and specificity: Choose if all significant observations agree with each other | ||
| + | *Clear function | ||
| + | *Clear specificity | ||
Revision as of 15:33, 11 September 2008
Alternative ORFs
Q: What if there's a possible Shine-Dalgarno sequence and start codon on the opposing strand in the middle of the gene you're working on? Do you assume that the computer has already marked it as a possible gene or do youhave to examine it as well?
A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring.
Alternative ORFs'
Q: What if there's a possible Shine-Dalgarno sequence and start codon on the opposing strand in the middle of the gene you're working on? Do you assume that the computer has already marked it as a possible gene or do youhave to examine it as well?
A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring.
Q: How do we rate our judgment calls? Can we indicate confidence levels?
A:Confidence levels (listed low to high)
- Hypothetical protein: choose if selected "hypothetical protein" under "gene product"
- Conserved hypothetical protein: choose if selected "conserved hypothetical protein" under "gene product"
- Not enough info to select "Family Membership" or "Function unclear"
- no domains identified
- no family membership)
- Family membership: Choose if conserved hypothetical protein identified via PFam or TIGRfam as belonging to a protein family but function and specificity are unclear.
- Function unclear: Choose if
- protein domain is identified
- protein function is unclear
- if "putative" or "possible" or "predicted" occur in all the significant Tigrfam, COG, or PFAM names
- Specificity unclear: Choose if only more general information on the function of a protein family is available
E.g., ABC transporter (but can't predict substrate) E.g., Histidine kinase (but can't predict target response regulator) High confidence in function and specificity: Choose if all significant observations agree with each other
- Clear function
- Clear specificity
