Hello everyone,
I have miRNA data generated through ION PGM. I am using SHRiMP software for mapping. I want to know how exactly SHRiMP algorith works
It is written that by default it makes 3 seeds with weight 12
seed1: 11110111101111
seed2: 1111011100100001111
seed3: 1111000011001101111
1. I want to know if this is the only pattern it makes seeds or it makes seed
according to our data.
2. Now will it match all the seeds and in what order. If out of three two seeds match and one does not match then will it consider that seed or will it be discarded.
3. when is the extension of these seeds take place??
Hoping for a positive response.
Neha
I have miRNA data generated through ION PGM. I am using SHRiMP software for mapping. I want to know how exactly SHRiMP algorith works
It is written that by default it makes 3 seeds with weight 12
seed1: 11110111101111
seed2: 1111011100100001111
seed3: 1111000011001101111
1. I want to know if this is the only pattern it makes seeds or it makes seed
according to our data.
2. Now will it match all the seeds and in what order. If out of three two seeds match and one does not match then will it consider that seed or will it be discarded.
3. when is the extension of these seeds take place??
Hoping for a positive response.
Neha
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