We further considered only cases where the known genes were coding and well annotated, as indicated by a RefSeq accession prefix of "NM_".
In summary, we found 6016 expressed genes for C. albicans and 5972 for C. dubliniensis of which 5541 and 5440 were coding and already annotated genes, respectively (Table 1, Figure 1A).
Detailed notes and summaries of these interviews were uploaded, coded and annotated using Atlas.ti (Scientific Software Development GmbH, Berlin) to identify recurrent themes from the interviews.
For each de novo assembly, coding sequences were predicted and annotated using the rapid prokaryotic genome annotation tool, Prokka (Seemann, 2014).
To this end, chromatin states and novel functional elements of the histone code [ 30] have been inferred and annotated, respectively, from histone modifications acting in a combinatorial fashion by using multivariate hidden Markov models [ 2, 31, 32], dynamic Bayesian networks [ 33, 34], or unsupervised machine learning [ 35].
A total of 1,400 coding regions were predicted and annotated.
In total, 4,579 coding sequences were detected and annotated by using the National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).nih.gov/genome/annotation_prok/
A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated.
Analysis of RDIP-seq, RNA-seq, and code for all figures are included and annotated at: https://github.com/GreallyLab/Nadel-et-al.-2015 //github.com/GreallyLab/Nadel-et-al.-2015 //github.com/GreallyLab/Nadel-et-al.-2015 //github.com/GreallyLab/Nadel-et-al.-2015
While improvements of the CHO-K1 genome annotation are still underway, there are 21,610 coding sequences annotated as of this publication.
