Microsatellites Explorer Help Page

This is the homepage of Microsatellites Explorer. It is comprised of high level metadata about the reasearch done, mainly statistics by biological domain , by repeating sequence and biological species:

From here you can navigate to other pages using the navigation bar , or you can navigate to the statistics per domain using the pie chart legend items

Navigation Bar:

Legend Items:

By clicking the legend items we are presented with the statistics per biological domain page. As the name implies, this page is used to perform a statistical analysis on the most relevant properties per domain and a further analysis per biological organism. Another way to access the different domains is through the Navigation Bar > Explore Domains

The domain metadata are organized at the upper part of the page whereas the organismal analysis is presented as a table on the lower part.

By clicking the Explore item at the navigation bar we are presented with a page that is used to effectively search , access and download parts of the Short Tandem Repeats dataset we produced. This page consists of some features that we implemented to explore the dataset. These are:

Advanced filtering is used to perform rich querying using all the available columns present on the accession metadata. For example find every accesson that comes from the domain of Bacteria and has more than 1 Chromosome and short Tandem Repeats present:

The quick search feature is used to search on the most frequently used columns, for example: organism_name=Homo Sapiens

We can then click on the accession id button of a specific row and navigate to the tandem repeats page of this specific accession. Here we can see calculations on tandem repeats , accession metadata, graphs about the distribution on tandem repeats units lengths and cross references to other public sources. We can also see where the short tandem repeats are present at the genome , Chromosome , Start , End:

An analysis and visualization per chromosome that the user selects provides the user with the ability to inspect the different STR unit lengths along with an arbitrary presentation of the unit sequences using unique coloring and a magnitude number to denote the gap between consecutive STR sequences

Another view of the same data ( NCBI organismal genomes ) is an aggregation of the different assemblies based on Organism Name. This can be accessed through Explore > Organisms

By clicking the organism name button we are being redirected to the aggregated analysis done on the organism for the different assemblies. Here we can gain a high level overview about STRs across assemblies and Inspect Filter and Download the raw files.

In order to access the Human Pangenome Table with the 95 human genomes including their STR metadata you go to Explore > Human Pangenome Project (HPP)

By clicking the button with the human genome on the left side of the table we are redirected to a page similar to the NCBI genome assemblies where the full human genome is analyzed in the context of short tandem repeats. Here as the headings imply we have some general metadata and some metadata about STRs.

Given the importance of genes on the human genome we implemented a feature to perform Short Tandem Repeat searches on genes based on Gene ID along with a bar plot for the top 5 most dense genes in terms STRs :

The same design principle is followed for the Telomere-to-Telomere genomes that are accessed through Explore > Telomere-to-Telomere Organismal Genomes:

We can then navigate to the specific assembly by clicking the blue button with the accession_id on the left

Finally you can use the downloads page to download the dataset as a whole in three different formats depending on the use. For example CSV for spreadsheet use, JSON for app development and Parquet.snappy for HPC use.