I am trying to understanding a couple of the settings in GS assembler, the alignment identity score and alignment difference score. In the manual, I found the following definitions but I can't get my head around what they mean:
Alignment identity score : When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Should be a value >=0 and the default is 2.
Alignment difference score : When multiple overlaps are found, the per-overlap column difference score used to sort the overlaps for use in the progressive multi-alignment.Should be a value <=0 and the default is -3.
What does this really mean?
Cheers, Joseph
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Are you using GSMapper or GSAssembler?
The definitions you posted is for GSAssembler. For GSMapper the definitions are:
Alignment identity score – When overlaps are extended during an alignment, this is the per-overlap-column identity score used to calculate the overall score for the alignment
Alignment difference score – When overlaps are extended during an alignment, this is the per-overlap-column difference score used to calculate the overall score for the alignment
I don't really know what they mean though.
Are you using GSMapper or GSAssembler? The definitions you posted is for GSAssembler. For GSMapper the definitions are: Alignment identity score – When overlaps are extended during an alignment, this is the per-overlap-column identity score used to calculate the overall score for the alignment. Alignment difference score – When overlaps are extended during an alignment, this is the per-overlap-column difference score used to calculate the overall score for the alignment I don't really know what they mean though. – DK 0 secs ago
Are you using GSMapper or GSAssembler? The definitions you posted is for GSAssembler. For GSMapper the definitions are: Alignment identity score – When overlaps are extended during an alignment, this is the per-overlap-column identity score used to calculate the overall score for the alignment Alignment difference score – When overlaps are extended during an alignment, this is the per-overlap-column difference score used to calculate the overall score for the alignment. I don't really know what they mean though. – DK 0 secs ago
Are you using GSMapper or GSAssembler? The definitions you posted is for GSAssembler. For GSMapper the definitions are: Alignment identity score – When overlaps are extended during an alignment, this is the per-overlap-column identity score used to calculate the overall score for the alignment Alignment difference score – When overlaps are extended during an alignment, this is the per-overlap-column difference score used to calculate the overall score for the alignment. I don't really know what they mean though.
Thanks for pointing that out. I have made the edit. I really don't understand what the definition means, I would understand as much if it was in a different language.