question about Modeling with cryo-EM compare.
When you read the second part of this tutorial at http://salilab.org/modeller/ncmi_2008/select.html. How do you read this table, or is there any function in modeller that use the table and output sequence identity.
Sequence identity comparison (ID_TABLE):
Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length).
1b8pA @11y7tA @11civA @25mdhA @27mdhA @23d5tA @21smkA @2 1b8pA @1 327 201 146 152 152 249 50 1y7tA @1 61 327 158 170 160 210 58 1civA @2 45 48 374 140 304 148 55 5mdhA @2 46 52 42 333 140 164 58 7mdhA @2 46 49 87 42 351 148 50 3d5tA @2 78 65 46 51 46 321 50 1smkA @2 16 19 18 19 16 16 313
I am not able to read the this table manually and I can not see how I can extract sequence_identity from it.
Best regards Knut J
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On 1/12/10 6:29 AM, Knut J Bjuland wrote: > When you read the second part of this tutorial at > http://salilab.org/modeller/ncmi_2008/select.html. How do you read this > table, or is there any function in modeller that use the table and > output sequence identity. > > Sequence identity comparison (ID_TABLE): > > Diagonal ... number of residues; > Upper triangle ... number of identical residues; > Lower triangle ... % sequence identity, id/min(length).
Just like it says, the upper triangle tells the number of identical residues, the diagonal the number of residues and the lower triangle the sequence identity.
> 1b8pA @11y7tA @11civA @25mdhA @27mdhA @23d5tA @21smkA @2 > 1b8pA @1 327 201 146 152 152 249 50 > 1y7tA @1 61 327 158 170 160 210 58 > 1civA @2 45 48 374 140 304 148 55 > 5mdhA @2 46 52 42 333 140 164 58 > 7mdhA @2 46 49 87 42 351 148 50 > 3d5tA @2 78 65 46 51 46 321 50 > 1smkA @2 16 19 18 19 16 16 313 > > I am not able to read the this table manually and I can not see how > I can extract sequence_identity from it.
For example, the lower (bottom left) triangle shows you that the sequence identity between 1b8pA and 1smkA is 16%, between 11y7tA and 3d5tA is 65%, and so on.
Ben Webb, Modeller Caretaker
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Knut J Bjuland -
Modeller Caretaker