2.4 Tool-wide comparison
MeStudio provides a novel amount of feature-level information that is
not present in other widely used genomic software packages. For
instance, Bedtools (https://bedtools.readthedocs.io/en/latest/) is a
well-known toolset for genomic applications through which it is possible
to detect methylation features regarding CpG island, but it is not
possible to extract information about CDS, nCDS, tIG and US regions as
it does not provide any figure about methylated motif occurrences.
Bioconductor also supplies packages that can be used for methylation
analysis such as “GenomicRanges ”
(https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
and “motifmatchr ”
(https://bioconductor.org/packages/release/bioc/html/motifmatchr.html).
GenomicRanges allows to split the genome in predefined intervals but no
information about the genomic feature is produced. The packagemotifmatchr allows to find motifs along the genome but no gene or
protein annotations are included in the output. Moreover, MeStudio
simply takes as input for the motifs a text file which is a more
user-friendly format compared to the one required by motifmatchr .
Table 1 provides a comparison of the features of MeStudio and possible
alternative tools.