Author: Marie Hoffmann; Michael T. Monaghan; Knut Reinert
Title: PriSeT: Efficient De Novo Primer Discovery Document date: 2020_4_7
ID: 3b3hv53b_35
Snippet: Having computed the FM index over the library, we can now submit queries with varying values of k. GenMap's frequency computation of k-mers is based on an algorithm described by Derrien et al. (2012) , but introduces runtime improvements by cutting redundant searches (Pockrandt et al., 2019) . GenMap provides location information of each k-mer by outputting the sequence identifier SeqID referring to the library sequence where a k-mer has been fou.....
Document: Having computed the FM index over the library, we can now submit queries with varying values of k. GenMap's frequency computation of k-mers is based on an algorithm described by Derrien et al. (2012) , but introduces runtime improvements by cutting redundant searches (Pockrandt et al., 2019) . GenMap provides location information of each k-mer by outputting the sequence identifier SeqID referring to the library sequence where a k-mer has been found and a relative position index SeqPos. These locations are collected in the Locations map (see Algorithm 2) with k-mers as keys and an occurrence vector as value.
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