How splice-aware aligner (RNA-Seq) deal with long gap (intron) penalty
A pre-defined gap penalty is usually used during DNA sequence alignment. However, In RNA-Seq the intron gap can be really long. I think usual gap penalty (for example affine) does not apply in such situation. So How do splice-aware aligners treat such gaps during matrix scoring?
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How a tool solves this problem is specific to the aligner and would most likely be described in the documentation of the aligner of interest - have you tried looking there?
In addition to the documentation and papers describing the tool, the ultimate description of the methods implemented in a tool is its source code.