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--- blog:2008:08:22faq_questions_about_the_definition_of_cath_code [2008/08/22 08:31] – created sillitoe
+++ blog:2008:08:22faq_questions_about_the_definition_of_cath_code [2015/08/17 18:36] (current) – sillitoe
@@ Line 1: / Line 1: @@
+====== FAQ: Questions about the definition of CATH code  ======
+The following is a reply from a recent email that may provide a useful explanation to others regarding the CATH code numbering with sequence clusters (SOLID).
+Received on Aug 21, 2008 (reproduced with permission)
+<code>
+Hi, CATH team:
+Upon reading the original paper published in 1997 and visiting your website, I am
+still confused about the definition of CATH code in sequence family levels. Take
+the CATH 3.1 reflected by these three below proteins as a example, my questions of
+them were as following:
+) the code in CATHSOLI level of 2a8vA01 and 1a8vA01 are all the same, but why
+their codes in D level were different?
+    Does 2a8vA01 and 1a8vA01 not belong to the same s100 family?
+) the code in CATHSO  ID level of 1a8vA01 and 1a62001 are all the same, but why
+their codes in L level were different?
+    If 1a8vA01 and 1a62001 are 100% sequence identical, why they were assigned to
+    different 95% sequence group?
+Sincerely.
+backy
+%   60%   95%   100%
+            C    A     T     H      S     O     L     I     D
+a8vA01     1    10   720    10     2     1     2     1     3    47 2.400
+a8vA01     1    10   720    10     2     1     2     1     1    49 2.000
+a62001     1    10   720    10     2     1     1     1     1    44 1.550
+</code>
+The reply on Aug 21, 2008
+<code>
+Hi Backy,
+Thanks for getting in touch with us, hopefully I can answer your questions below:
+) the code in CATHSOLI level of 2a8vA01 and 1a8vA01 are all the same, but why
+       their codes in D level were different?
+The D level stands for "Domain Count" and is just there to provide a unique code
+for every domain - so if two domains are identical (i.e. they share everything up
+to the I, or 100% Identical, code) then we use the D level to differentiate
+between them - this is just a sequential counter.
+        Does 2a8vA01 and 1a8vA01 not belong to the same s100 family?
+Yes, they do - they share up to the I count so they are 100% identical - as mentioned
+above - the domain level is just a counter to differentiate between domains in the
+same I cluster.
+) the code in CATHSO  ID level of 1a8vA01 and 1a62001 are all the same, but
+       why their codes in L level were different?
+You need to bear in mind that CATH is a tree-like hierarchy with the trunk of the
+tree represented on the left of the CATHSOLID classification (e.g. the C code) and
+the leaves of the tree on the right (e.g. the D code). In the example you give above
+- you have to read the CATH codes from left to right and stop the first time one of
+the codes differs. In this case, they differ at the 'L' code so they are in different
+S95% clusters. It doesn't matter that the numbers after this (I, D) are the same as
+they are talking about different branches of the tree.
+        If 1a8vA01 and 1a62001 are 100% sequence identical, why they were assigned
+        to different 95% sequence group?
+The simple answer is that they aren't 100% identical - they have a seq id of 94.7%
+so they are in different L codes. As mentioned above, the I and D happen to be the
+same, but that doesn't mean anything if the L code is different (CATHSOLID needs to
+be read from left to right).
+So for the following three domains:
+a8vA01 1.10.720.10.2.1.2.1.3
+a8vA01 1.10.720.10.2.1.2.1.1
+a62001 1.10.720.10.2.1.1.1.1
+The tree/hierarchy would look something like:
+C                   1
+A                  10
+T                  720
+H                  10
+S                   2
+O                   1
+L       1                        2
+I       1                        1
+D       1                  1           3
+a62001           1a8vA01     2a8vA01
+This seems like a good question/answer to add to our FAQ section of the website - would you mind?
+Best wishes,
+Ian Sillitoe
+CATH Team
+</code>

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