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_8
Snippet: Because this split size is based on the alignment and since dashes in the alignment are not counted in amplicon length, actual amplicons may be substantially shorter than the split size . This is likely to happen for poorly aligning regions or regions in which there are insertions or deletions in a subset of the sequences. To compensate for this, one should select that is larger than the actual amplicon lengths desired, particularly if the length.....
Document: Because this split size is based on the alignment and since dashes in the alignment are not counted in amplicon length, actual amplicons may be substantially shorter than the split size . This is likely to happen for poorly aligning regions or regions in which there are insertions or deletions in a subset of the sequences. To compensate for this, one should select that is larger than the actual amplicon lengths desired, particularly if the length of the MSA is much larger than the average genome length.
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