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"Your clothes, bedding and even the dishes' base pattern is a market which is exponentially growing at $240 billion, in the age of millennials and 'hipsterdom' where people can't stand being copied and have something original.
A base pattern is regarded as the sequence of the pairs (position, nucleotide) for all HSPs found in the read.
A base pattern is assigned to a genome if at least 50% (a user-specified parameter) of its bases at HSP positions match with the corresponding diploid genome.
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Once a list of valid base patterns is obtained for the current gene, HANDS assigns the base patterns to individual genomes using the SBS data for the diploid progenitors.
A basing pattern is often a sign of accumulation by large institutions and can be identified by its sideways oscillations.
In step 2, base patterns that are a result of sequencing error or embedded in other base patterns are removed.
Once base patterns are obtained all further processing is done on these patterns and not on reads.
In step 3, base patterns are assigned to one or more subgenomes based on their similarity with the corresponding diploid.
In step 4, base patterns are prioritized based on their percentage identity with the diploids, and bases are assigned to each subgenome iteratively discarding base patterns that contradict with the already assigned bases.
Tetra-, penta- and hexa-nucleotide SSRS were only present in small numbers in the obtained transcriptome sequences from the two celery varieties and their base patterns were quite complex and were not subjected to detailed analysis.
Clearly, the upstream base composition abundance pattern is not conserved among the four protists.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com