BFAST scoring matrix

[gene coder]

Hello folks,

I wonder what the default scoring matrix is in BFAST. I can only find information on instructions of how to set one, but there is no information regarding the default.

[gene coder]

Problem solved! I have managed to find it in the source file BLibDefinitions.h. It is also in the file bfast-book.pdf.

/* Scoring matrix defaults */
#define SCORING_MATRIX_GAP_OPEN -175
#define SCORING_MATRIX_GAP_EXTEND -50
#define SCORING_MATRIX_NT_MATCH 50
#define SCORING_MATRIX_NT_MISMATCH -150 
#define SCORING_MATRIX_COLOR_MATCH 0
#define SCORING_MATRIX_COLOR_MISMATCH -125

I am looking for long indels, if anyone is wondering. That means a lower gap extension score.

[nilshomer]

The "-x" option in "bfast localalign" can also be set.

How long is "long" indels? You can try lowering the gap extension penalty.