[Next-Generation Sequencing Book]

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[ Ticket #195 ] Longest sequence first???
Date:
08/19/04 07:28
Submitted by:
dmb 		Assigned to:
liwz
Category:
Clustering 		Priority:
9
Ticket group:
Critical 		Resolution:
Resolved
Summary:
Longest sequence first???
Original submission:


CD-HIT should cluster from the longest sequence first, taking that sequence to be the representative.

This dosn't appear to happen in a very simple test case...


>15982
kkekspkgkssispqarafleqvfrrkqslnskekeevakkcgitplqvrvwfinkrmrsk
>79112
aaaaaispqarafleqvfrrkqslnskekeevakkcgitplqvrvwfinkrmrsk
>15981
ispqarafleqvfrrkqslnskekeevakkcgitplqvrvwfinkrmrs


(Which is easy to align...

>15982
kkekspkgkssispqarafleqvfrrkqslnskekeevakkcgitplqvrvwfinkrmrsk
>79112
------aaaaaispqarafleqvfrrkqslnskekeevakkcgitplqvrvwfinkrmrsk
>15981
-----------ispqarafleqvfrrkqslnskekeevakkcgitplqvrvwfinkrmrs-

)


The longest sequence (SCOP SUNID 15982) should not clustr with 79112 at 100 percent identity threshold, but should then cluster with 15981 at 100%.

However the result of the 100% clustering are...

>Cluster 0
0 61aa, >15982... *
>Cluster 1
0 55aa, >79112... *
1 49aa, >15981... at 100%

For some reason 79112 is clustering with 15981 at 100 percent *first*, so when 15982 comes along it dosn't see 100% identity to 15981 (behind its representative 79112), and forms a cluster on its own.

The correct clustering should be

>Cluster 0
0 61aa, >15982... *
1 49aa, >15981... at 100%
>Cluster 1
0 55aa, >79112... *

What is the problem here?
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Comment Date By

I guess that that's the way that the code is written. (I was wondering about it too and it seems to be different from the descritption described in the paper. So I just checked their codes ).

A sequence seems to be compared to the shortest representative sequence first. Therefore, 15981 is compared to 79112 first. And they are identical above the specified threshold, 15981 is clustered to 79112 without being compared to 79112.






01/07/06 21:28 unset
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Ticket change history
Field Old value Date By
status_id Open 05/16/11 00:37 liwz
resolution_id Unset 05/16/11 00:37 liwz
close_date 12/31/69 19:00 05/16/11 00:37 liwz
priority 8 05/24/05 11:32 dmb
status_id Unset 08/19/04 07:29 dmb
priority 5 08/19/04 07:29 dmb
assigned_to unset 08/19/04 07:29 dmb

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