  Motivation: The regulation of gene expression during tissue development is
extremely complex. One of the key regulatory mechanisms of gene expression
involves the recognition of regulatory motifs by various proteins in the
promoter regions of many genes. Localisation of these motifs in proximity to
the transcription start site (TSS) or translation start site (ATG) is critical
for regulating the initiation and rate of transcription. The levels of
transcription of individual genes, regulated by these motifs, can vary signifi
cantly in diff erent tissues and developmental stages, especially during
tightly regulated processes such as sexual reproduction. However, the precise
localisation and visualisation of the regulatory motifs within gene promoters
with respect to gene transcription in specifi c tissues, can be challenging.
Results: Here, we introduce a program called GOLEM (Gene regulatOry eLEMents)
which enables users to precisely locate any motif of interest with respect to
TSS or ATG within the relevant plant genomes across the plant Tree of Life
(Marchantia, Physcomitrium, Amborella, Oryza, Zea, Solanum and Arabidopsis).
The visualisation of the motifs is performed with respect to the transcript
levels of particular genes in leaves and male reproductive tissues, and can be
compared with genome-wide distribution regardless of the transcription level.
Availability and implementation: GOLEM is freely available at
https://golem.ncbr.muni.cz and its source codes are provided under the MIT
licence at GitHub at https://github.com/sb-ncbr/golem.
