Sentence examples for choice of annotation from inspiring English sources

While recently published integrated software systems, such as DIYA [2] and the Genome Reverse Compiler [13], provide standalone packages for genome annotation, they do not have fully integrated and automated visualization tools and do not enable the full utilization of parallel computing, which significantly limits their choice of annotation tools.

Here we consider how the choice of annotation database affects expression estimation for methods that use a predefined reference transcriptome.

The fact that choice of annotation for mapping assignment is an unexpectedly important facet of RNA-seq analysis has also been reported by others [ 45].

However, it is clear that the annotation results obtained were very sensitive to both the query dataset and the choice of annotation source.

Altering parameters of the preprocessing steps, e.g., aligning procedure, summarization of reads, choice of annotation, and normalization techniques, can change the output of a gene expression analysis drastically.

We have aimed to highlight the effect on final annotation results that can arise from two aspects of analyses of whole genome (or whole exome) sequence data, namely, choice of transcript and choice of annotation software.

This has implications for the choice of reference annotation set to be used for estimation: more sensitive annotations, such as Ensembl, which contains 190 243 (release 66) human transcripts, should be preferred over more specific annotations, such as RefSeq [ 15], which contains 50 029 human transcripts, if the aim is to obtain accurate expression estimates.

Third, the choice of an annotation tool is largely dependent on the desired selection of variant annotations.

The choice of genome annotation directly affects gene expression estimation.

The impact of the choice of an annotation on estimating gene expression remains insufficiently investigated.

Gene quantification and differential analysis results are dependent upon the initial choice of gene annotation [ 19– 219.