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We used Geneious 6.1.7 (Biomatters 2013) to sort sequence reads by barcode and trim the restriction sites; we explored different strategies for trimming the sequences and found that they made no difference for the results.
The high degree of conservation in LD phase found in this sort sequence in almost breeds, independently of their geographic origin, could indicate that high levels of gene flow have occurred between populations following domestication, as is suggested by Kijas and coworkers [ 3], but also, a selection pressure exerted over this DNA region [ 28].
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The OTU clustering packages (e.g. CD-HIT-OTU) sort sequences by abundance and process them from high to low.
Based on the Illumina raw data, a custom Perl script was written to sort sequences from individual samples based on indexes and trimmed barcode sequences for faster processing.
Most methods introduced herein, including programs in CD-HIT package, Uclust and DNACLUST sort sequences by length and process them from long to short.
For this analysis, we sorted sequence reads into two pools based upon the presence or absence of the CCA tail.
The values of the key are arranged in a sorting sequence that is dependent on the type of key involved: alphanumeric key values are usually sorted in alphabetic sequence, while other types may be sorted on the basis of similarity in class, such as books on a particular subject or flora of the same genus.
Time sorted sequence of all these events combined together forms a simulated catalog.
This work could also propose an alternative way to immobilize a heterologous protein on the cell wall of B. subtilis using a fusion form of YhcR sorting sequence.
This result further indicates that the YhcR sorting sequence can be used to display recombinant proteins on the surface of B. subtilis cells.
In terms of application, this work demonstrated that the YhcR sorting sequence can be specifically used to display heterologous proteins on the cell-wall of B. subtilis cells.
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