ConSurfDB vs. ConSurf: Difference between revisions

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# Scroll down and click ''Homologues, Alignment, and Phylogeny''.

# Notice the number of sequences in the MSA (the number of "hits" upon which "calculations were conducted").

# '''To view the list of sequences in the multiple sequence alignment (MSA)''' from which the conservation pattern was determined, click on the count of hits upon which the calculations were conducted. (If fewer than 50 hits were used, it will probably be useful to do another run using a larger database: UniProt and NR are larger than the default UniProt90. Use the button "Select Run Parameters Manually".

# '''To view the list of sequences in the multiple sequence alignment (MSA)''' from which the conservation pattern was determined, click on the count of hits upon which the calculations were conducted.

# '''Get the Average Pairwise Distance (APD)''' by clicking "View Alignment Details". A value ~~> ~~~1.1 suggests that proteins with multiple functions were included in the multiple sequence alignment, which obscures conservation related to the function of your query protein. See [[Interpreting ConSurf Results]], where the APD is explained.

# '''Get the Average Pairwise Distance (APD)''' by clicking "View Alignment Details". A value close to, or larger than 1.0 suggests that proteins with multiple functions were included in the multiple sequence alignment, which obscures conservation related to the function of your query protein. See [[Interpreting ConSurf Results]], where the APD is explained.

If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest.

ConSurfDB vs. ConSurf: Difference between revisions

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@@ Line 35: / Line 35: @@
 # Scroll down and click ''Homologues, Alignment, and Phylogeny''.
 # Notice the number of sequences in the MSA (the number of "hits" upon which "calculations were conducted").
-# '''To view the list of sequences in the multiple sequence alignment (MSA)''' from which the conservation pattern was determined, click on the count of hits upon which the calculations were conducted. (If fewer than 50 hits were used, it will probably be useful to do another run using a larger database: UniProt and NR are larger than the default UniProt90. Use the button "Select Run Parameters Manually".
+# '''To view the list of sequences in the multiple sequence alignment (MSA)''' from which the conservation pattern was determined, click on the count of hits upon which the calculations were conducted. <!--(If fewer than 50 hits were used, it will probably be useful to do another run using a larger database: UniProt and NR are larger than the default UniProt90. Use the button "Select Run Parameters Manually".-->
-# '''Get the Average Pairwise Distance (APD)''' by clicking "View Alignment Details". A value > ~1.1 suggests that proteins with multiple functions were included in the multiple sequence alignment, which obscures conservation related to the function of your query protein. See [[Interpreting ConSurf Results]], where the APD is explained.
+# '''Get the Average Pairwise Distance (APD)''' by clicking "View Alignment Details". A value close to, or larger than 1.0 suggests that proteins with multiple functions were included in the multiple sequence alignment, which obscures conservation related to the function of your query protein. See [[Interpreting ConSurf Results]], where the APD is explained.
 If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest.