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Fri Jan 4 07:58:09 2013 UTC (6 years, 9 months ago) by golsen
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Update the description of the sim table cell colors.

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<TITLE>Explanation of "Region in ..." Colors</TITLE>
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<H1>Explanation of "Region in ..." Colors</H1>

In the protein similarities table, the table cells that describe the sequence regions responsible for the similarity are colored to reflect the extent and location of the similarity.  The coloring is intended to provide a quick visual cue as to the nature of the similarity, and help in assessing broad classes of possible relationships (most particularly, whether there are reasons to doubt that these sequences have the same function).
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The intensity (saturation) of the color depends on the fraction of the sequence that is covered by the similarity.

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If the similarity extends over at least 90% of the sequence, then the table cell background is white.
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If the similarity covers less than 90% of the sequence, then there is a background color.  The shorter the region of similarity, the more intense the color.
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The color (hue) of the cell depends of which region of the sequence is similar.

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The colors go from red through green to blue as the region of matching moves from the beginning to the end of the sequence.
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The color is determined by the position of the matching region within the sequence. A match that extends all the way to the beginning, but does not reach the end is fully red (with the saturation depending on the amount of the sequence covered). A match that extends all the way to the end, but does not include the beginning is fully blue (with the saturation depending on the amount of the sequence covered).
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Taken together, the colors of the subject sequence (left column) and the query sequence (right column) tell a story.

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<TR><TH>Subject<BR />color</TH><TH>Query<BR />color</TH><TH>Some possible interpretations</TH></TR>

<TR><TD>White</TD><TD>White</TD><TD>Both sequences match over (essentially) their full length.</TD></TR>

<TR><TD>White</TD><TD>Colored</TD><TD>The subject sequence is shorter than the query sequence.  The subject sequence might be a fragment of a protein (perhaps the result of a sequencing error, or running off the end of a contig).  Alternatively, the query sequence might be a multifunctional protein, and the subject sequence does not have all of the functions.  A related situation is when proteins found as one peptide in some organisms are found in two separate peptides in others.</TD></TR>

<TR><TD>Colored</TD><TD>White</TD><TD>The query sequence is shorter than the subject sequence.  The query sequence might be a fragment of a protein (perhaps the result of a sequencing error, or running off the end of a contig).  Alternatively, the subject sequence might be a multifunctional protein, and the query sequence does not have all of the functions.  A related situation is when proteins found as one peptide in some organisms are found in two separate peptides in others.</TD></TR>

<TR><TD>Colored</TD><TD>Same color</TD><TD>The query and subject are of similar lengths, <B>and</B> the region of similarity is the same in both sequences.  This often happens when analyzing sequences that are distantly related, or when some part(s) of the molecule diverge particularly quickly.</TD></TR>

<TR><TD>Colored</TD><TD>Different color</TD><TD>This happens when comparing two partial sequences that cover different parts of a molecule.  Alternatively, the similarity could be due to a conserved motif shared by two molecules of quite different function.</TD></TR>

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Closing thoughts:
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In considering whether two proteins have the same function, one would prefer that the similarity cover essentially the entirety of both molecules (little or no color).  When this is not true, one would prefer that the colors match as closely as possible.

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