The DNA Visualizer tool for feature exploration on SequenceServer

What is the DNA Visualizer?

The DNA Visualizer serves as a valuable tool for the annotation process for genomes, plasmids and other DNA sequences. Leveraging Bakta (Schwengers et al, 2021), SequenceServer simplifies the annotation workflow, allowing you to analyze your data quickly.

Annotation involves the identification and labelling of DNA features such as, genes, regulatory elements, and functional components like binding domains of protein-coding sequences. Bakta is capability of discerning known identical protein sequences (IPS) sourced from RefSeq and UniProt, as well as small proteins/short open reading frames (sORF). Beyond protein annotation, its functionality includes the identification of non-coding RNA, cis-regulatory regions, oriC/oriV/oriT, assembly gaps, and a range of features such as tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS, and pseudogenes.

DNA Visualizer is accessible to SequenceServer’s cloud users, located at the top and bottom of the BLAST interface page.

You can find the SequenceServer DNA Visualizer tool either in the top banner or down at the bottom of the web page.

FASTA DNA sequences as input for genomic feature annotation

The DNA Visualizer takes DNA sequences only as input and are copy-pasted into the query box. These DNA sequences can be anything from bacterial genomes, plasmids (complete or draft assemblies) and gene sequences.

BLASTN output results can be analyzed DNA Visualizer

Alternatively, following a BLASTN analysis through the Run BLAST interface, you can choose to run the DNA Visualizer to analyze your BLAST hits. This can be a powerful way to identify whether your aligned regions possess annotated functionality.

Once you've performed a BLAST search you can access the DNA visualizer with the 'Explore DNA Features' tab, which will analyse your hit sequence.

Plasmid and genome feature exploration with DNA Visualizer

Analyzing plasmid features

A complete plasmid sequence can be analyzed with DNA Visualizer to annotate and explore various elements. The example below includes a bacterial plasmid containing TEM-116, a broad-spectrum beta-lactamase found in many species of bacteria.

By using DNA Visualizer, in this plasmid we are able to see:

All this information helps to understand the structure, function, and utility of plasmids in various molecular biology applications, for example:

SeqeunceServer DNA Visualizer is great for plasmid annotation, showing different features like genes, restrection enzyme sites and more!

Bacterial genome annotation

The genome annotation process can be a complex and time consuming process. DNA Visualizer makes annotation of bacterial genomes and collection of downstream files simple.

Here we will annotate the genome of the bacteria Candidatus Carsonella ruddii using the GenBank assembly version that has the accession GCA_000287275.1. We can simply paste this genome sequence into DNA Visualizer and annotate the genome. And there it is, an annotated genome! As you can see, many features are annotated, including protein coding genes.

On the left-hand side there is a drop-down menu with a range of options for different visualizations such as circular/linear views, zooming, showing the positions, and both DNA strands. We can also select to download all (or some of) the annotation files. These files are very useful in downstream analysis, for example the GFF3 files for RNAseq read mapping, or the nucleotide and protein FASTA files for creating a custom BLAST database for our new annotation so we identify homology relationships.

Once you have the annotation you can manipulate the images and download all the associated annotation files from the drop down menu on the left.

Explore DNA Visualizer features output

As mentioned above, DNA Visualizer can also be reached from the BLAST output, which takes you to visualise the hit’s location in the BLAST subject.

The example below shows the location of the gene Cinnamyl alcohol dehydrogenases (CAD) which encodes an AP-1 type transcription factor within the bakers yeast Saccharomyces cerevisiae located on chromosome III.

This demonstrates another use of DNA Visualizer, assessing the genetic location of a gene of interest which can be advantageous for functional annotation, gene mapping, and comparative genomics to name a few. These annotation features are usually formatted in the GFF3 files, which can be downloaded from the drop-down menu on the left-hand side.

SequenceServer DNA Visualizer can identify yeast genome features and gives their location

Possible insights with DNA Visualizer

As DNA Visualizer runs a genome annotation/analysis with Bakta, it is able to provide a wide range of insights, such as the following.

Happy BLASTing!

Schwengers O., Jelonek L., Dieckmann M. A., Beyvers S., Blom J., Goesmann A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11).

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