General Questions - Revision history

MaCampbell at 15:36, 11 September 2008

2008-09-11T15:36:09Z

MaCampbell at 15:35, 11 September 2008

2008-09-11T15:35:28Z

MaCampbell at 15:34, 11 September 2008

2008-09-11T15:34:46Z

MaCampbell at 15:33, 11 September 2008

2008-09-11T15:33:49Z

MaCampbell at 15:33, 11 September 2008

2008-09-11T15:33:21Z

Salt at 19:13, 10 September 2008

2008-09-10T19:13:29Z

New page

'''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>

@@ Line 23: / Line 23: @@
 **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)
+*'''Specificity unclear''':  Choose if only more general information on the function of a protein family is available
-High confidence in function and specificity:  Choose if all significant observations agree with each other
+**e.g., ABC transporter (but can't predict substrate)
 **Clear function
 **Clear specificity

@@ Line 23: / Line 23: @@
 **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
+*'''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

@@ Line 13: / Line 13: @@
 A:Confidence levels (listed low to high)
-**'''Hypothetical protein''': choose if selected "hypothetical protein" under "gene product"<br>
+*'''Hypothetical protein''': choose if selected "hypothetical protein" under "gene product"<br>
-**'''Conserved hypothetical protein''':  choose if selected "conserved 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"
+**Not enough info to select "Family Membership" or "Function unclear"
-*no domains identified
+**no domains identified
-*no family membership)<br>
+**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>
+*'''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
+*'''Function unclear''':  Choose if
-*protein domain is identified
+**protein domain is identified
-*protein function is unclear
+**protein function is unclear
-*if "putative" or "possible" or "predicted" occur in all the significant Tigrfam, COG, or PFAM names<br>
+**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
+*'''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., ABC transporter (but can't predict substrate)
-E.g., Histidine kinase (but can't predict target response regulator)
+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 function
-*Clear specificity
+**Clear specificity

@@ Line 13: / Line 13: @@
 A:Confidence levels (listed low to high)
-#'''Hypothetical protein''': choose if selected "hypothetical protein" under "gene product"<br>
+**'''Hypothetical protein''': choose if selected "hypothetical protein" under "gene product"<br>
-#'''Conserved hypothetical protein''':  choose if selected "conserved 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

← Older revision		Revision as of 15:33, 11 September 2008
Line 3:		Line 3:

	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