Introduction to Ensembl Genome Browser (Tutorial) PDF

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Summary

Practical notes on Ensembl database and how to utilize this database for accessing useful information for research purposes....

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ENSEMBL Database link: https://asia.ensembl.org/index.html Purpose: Retrieval of gene annotation such as splice variants, gene ontology, genetic variations, gene expression and pathways. Performing Comparative genomics and regulation analysis.

*Entire analysis was performed on BDNF ( Homo Sapiens)

Introduction: ENSEMBL is a genome browser and a database for model organisms that allows comparative genomics, efficient genome data retrieval with various annotation features. Ensembl contains annotated genes, computes multiple alignment, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the variant effect prediction (VEP) for all supported species. The homepage of ENSEMBL is shown in the Figure 3.1

Figure 3.1 The homepage of ENSEMBL

Steps: ● I visited the homepage of Ensembl via the link:

https://asia.ensembl.org/index.html ● ● ● ● ● ● ● ● ● ●

From the homepage of NCBI, I clicked on the ‘view full list of all species’. When the list opened, I clicked on human species. Human search page opened, then I wrote BDNF (Human gene) in the search box. In the new window screen, information on BDNF gene appeared (Figure 3.2) which contains the description, locatio, transcription, CCDS, gene type, contigs etc. In transcript table, name of gene, transcript ID, bp, protein length, biotype, CDS, uniprot, refseq, match and flags are present. Figure 3.3 After that I clicked on the ‘slice variants’ from the given right side options. Then I clicked on the transcript comparison for further study of query genes. After this comparison, I clicked on the sequence and then on the genomic alignments. When the page for genomic alignments opened, I clicked on the ‘ select an alignment’ then on pairwise option and clicked on ‘primates. When a species name appeared I selected ‘Chimpanzee’ and then clicked on apply. [Results appeared on the screen.]

● After analyzing them I clicked on gene tree, gene gain/loss tree, orthologous/paralogous, gene ontology, genetic variation, genetic expression, pathway and regulation for further study of BDNF gene.

Location- Based Display: ● Went to Ensembl as explained in the previous steps and searched for the BDNF gene once again. ● When the page opened up for the gene, I clicked on ‘Location’. ● New results appeared on the screen. ● Then I clicked on the whole genome, region in detail, synteny, alignment (image/text) and region comparison for study of genes. Figure 3.4

BLAST/BLAT Went to Ensemble from the URL given above and again searched for BDNF . Then I clicked on Sequence, option given on the right side of the page. The page opened up and then I clicked on ‘BLAST this sequence’. A new screen appeared where I selected species by clicking on the ‘Add/Remove species' button. Figure 3.5 ● Then I selected ‘DNA database’ and ‘genomic sequence’ and clicked on the ‘Run’ button.

● ● ● ●

[Results appeared on the screen. Figure 3.6]

Figure 3.2: ENSEMBL information page for BDNF gene

Figure 3.3: Transcript Table of BDNF gene

Figure 3.4: Chromosomal location of BDNF Human gene

Figure 3.5: Selected species for Ensembl BLAST

Figure 3.6: Ensembl BLAST results...