Author: Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.; Peña, José; Hysom, David A.; Borucki, Monica K.
Title: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes Document date: 2014_8_3
ID: 1e44usl6_10
Snippet: The primers can be run in separate singleplex reactions for each split region, or, alternatively, primers for all regions can be combined in a large multiplex after the large set is checked for primer dimers that could occur between primers from different regions. Combining primers for all regions is calculated using Unafold [6] . 2 Low complexity regions (repetitive sequence) are excluded from consideration as primers by setting a minimum entrop.....
Document: The primers can be run in separate singleplex reactions for each split region, or, alternatively, primers for all regions can be combined in a large multiplex after the large set is checked for primer dimers that could occur between primers from different regions. Combining primers for all regions is calculated using Unafold [6] . 2 Low complexity regions (repetitive sequence) are excluded from consideration as primers by setting a minimum entropy threshold for a primer candidate. The entropy of a sequence was computed by counting the numbers of occurrences of , , . . . , of the 64 possible trimers in the probe sequence, and dividing by the total number of trimers, yielding the corresponding frequencies , . . . , . The entropy is then given by the sum of − log 2 where the sum is over the trimers t with ̸ = 0.
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