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help.qmd
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---
title: "Website useage help"
---
This website presents the comprehensive information related to
the RNA structure predictions. The website offers the following
main sections (see entries in the blue navigation bar on the top of the website):
## CRS-Cyanobacteria
The landing page briefly describes the study and contains links
to the main computational tools, the citation reference, and
a table with an overview over the number of predicted
conserved RNA structures (CRSs).
## Browse CRSs
The browser page allows a user to filter the predicted CRSs by
taxonomy (search area in the top right table),
scores and pathway associations (check boxes in the top left).
All CRSs that fit the user selection are shown in the table below.
The main result table also has a search field that allows the user
to search for gene names, ortholog identifiers, or CRS identifiers.
A click on the header of each table allows to re-arrange the rows
by the score of the clicked column.
Hoovering over the red information circles shows additional information
to each respective entry.
Clicking on the blue underlines CRS identifier in the lower table
naviages a user to details of the corresponding CRS in the next
website section.
## CRS details
This section shows all details associated with a CRS that a user
selected either in the prior browser section or from the drop down
box.
The shown information includes all scores, potential
pathway associations from the orthologous gene adjacent to which
the CRS was perdicted, all occurences of alignment sequences in the genomes,
an overview over which species contain alignment sequences,
and predicted transcriptional activity.
The details page also shows the conserved RNA structure predicted
by CMfinder with R-scape significant compensatory base pairs highlighted
in green. The structure figures were generated with R2R.
The legend to these structures is as follows (adapted from the R2R handbook):
<center><img src="r2r.svg" width = '70%'/></center>
## Alignments
This sections shows the alignments the predicted CRSs.
The nucleotide positions are colored according to the JalView default
scheme, that is
<font color='green'>adenine in green</font>,
<font color='orange'>cytosine in orange</font>,
<font color='red'>guanine in red</font>,
and
<font color='blue'>uracil in blue</font>.
The sequence identifiers on the left side are
dot separated combination of the NCBI taxonomy ID,
the BioSample identifier, and the Genbank Accession of the respective
plasmid.
The conserved RNA structures are shown below the alignment.
## Known structures
The novelty of CRSs was assessed to known RNA structures that
were annotated via a homology search with CMsearch.
This website section lists all hits for bacterial Rfam families that
overlapped the search regions in which this study screened for
RNA structures. A user can interact with this website section
in a similar manner as the CRS browser.