Strand NGS-Annotation toolbox for organisms

Our planet accommodates a variety of life with their genes: from civilized humans to the colonized bacteria, from infamous mosquito to the cutest puppies, and from golden rice to the greenest algae. Studying these species helps us in understanding the genetics of the species and population diversity and also other biomedical and bio technical applications.
Advancements in genome sequencing technology helps us with an improved understanding of all these organisms. The sequencing technologies produce a huge amount of data-reads (small fragments of the genome sequence), which are analyzed for transcriptional characterization and expression, potential biological markers, variants in genes, alternative splicing etc. This analysis requires a template or reference sequence and its annotation-description of the region of interest in the sequence; to baseline, compare and map our reads.

Why a Reference Sequence?
Read Sequences are like pieces of a non trivial jigsaw puzzle. These pieces could be arranged easily with the help of a reference picture or a template to work on. The same way, a read sequence can be analyzed easily with the help of a reference sequence or a template sequence. These template sequences are made by International consortium for each species by assembly of DNA sequences from one or multiple samples. With the help of scientists worldwide, most species have a reference genome.

Why so many Reference Sequences?
We do know that individual genomes are not identical and have variations. So we need an ideal and standard reference that accommodates these variations and hence the reference keeps getting updated along with its annotations. The reference genome and annotations are available in databases like RefSeq, Ensembl, UCSC. The frequent updates are differentiated with a version name, also called the genomic build or assembly. For example, builds of a mouse are mm10, mm9. And for each build the annotation sources get updated in annotation databases like RefSeq Genes and Transcripts, Ensembl, GO etc.

Fetching a Reference Sequences
Now we know, there are multiple builds from multiple databases and each build has a variation.How do we fetch this data and analyze them at convenience?
Strand NGS has a best solution to it. It has a repository of all these builds from different organisms and various databases which can easily be downloaded and used for analysis.

In Strand NGS, there is a specific option dedicated to it and is called Annotations.
1.Click on Annotations in menu bar and then click on Annotations Manager.
2.Go to List and select From Server
3.It shows a list of organisms with their annotation list. Check the boxes for the required annotations and select Update.
{The annotations are arranged according to organisms and are present in a hierarchical node manner with each annotation source as sub nodes and The storage space required for download is mentioned on the corner of the dialogue box}
4.Once updated the build is added as a node and you can view it.

Custom Build!
Wish to add your custom build? Go to the organism of choice and right click and select Add Build.A popup window appears with different options to add annotations

Now, How to analyze using the annotation?
1.Go to an existing project and in the menu bar, click on Project and click on New Experiment.
2.Choose Experiment name and Experiment type and click OK.
3.In metadata options, you can easily add annotations of your interest and then insert your samples.

Analyze your data with a plethora of visualizations after experiment creation. Now, it is easier to address questions posed on different organisms, their origin, and their genomic variations using Strand NGS.

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