Question: What Is The Alignment Identity Score And Alignment Difference Score In Gs Mapper/Newbler
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gravatar for Joseph Hughes
7.9 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

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

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Joseph Hughes2.7k

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.

ADD REPLYlink written 7.9 years ago by Damian Kao15k

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

ADD REPLYlink written 7.9 years ago by Damian Kao15k

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

ADD REPLYlink written 7.9 years ago by Damian Kao15k

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.

ADD REPLYlink written 7.9 years ago by Damian Kao15k

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.

ADD REPLYlink written 7.9 years ago by Joseph Hughes2.7k
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