Procedure 1: Locating the position of a gene
In Ensembl:
Search the internet link to the ensemble website: http://www.ensembl.org/index.html
On the Genome Browser located on the web page, select the human genome – GRCh38.p5 – to obtain various sub-topics about the genome. Type the name of the gene in the search box of the human genome webpage.
The MSRA homepage will contain a summarized description of the gene, including the including the location of the chromosome, its size, and the start and finish nucleotide.
In NCBI:
Search the link http://www.ncbi.nlm.nih.gov/ to obtain the NCBI homepage.
Type the gene name MSRA on the gene search box. From the list of search results, select the first option – MSRA (ID: 4482).
A web page displaying information about the gene will open. From the summary and facts presented in the genomic context table on the page, extract information about the location of the gene on the chromosome, its size, and start and finish nucleotides. From the paragraph, the start and finish positions of nucleotides on the gene are 10,054,224 and 10,428,891 respectively while the size of the gene is 394 Kb. The map position of the chromosome is 8p23.1.
Comparing the information on the two websites
Both websites provide easy access to and a brief outline information regarding the size of the gene and the map position of the chromosome. The information also includes UniProt and transcript details and describe other assemblies. Nevertheless, the information provided by the NCBI link is more detailed compared to the Ensembl link. It lists other research articles related to the topic, and the genomic context paragraph gives additional information on the number of exons. In contrast, Ensembl requires one to click the Sequence link and sift through other filters to obtain information on the sequence of introns and exons. These additional procedures are time-consuming, thus slowing down the search process.
Procedure 2: Getting details about the gene structure
In Ensembl:
On the human gene browser located on the web page, type the name of the gene.
Choose the MSRA human gene.
On the drop-down menu box located on the left of the summary web page, choose the sequence. This step displays information on the whole gene sequence, with the exons highlighted in red.
In NCBI:
Go to the link http://www.ncbi.nlm.nih.gov/
Navigate to the Genomic regions, transcripts, and products section on the page.
Procedure 3: Obtaining details on the homozygous SNP
In Ensembl:
Click the link http://www.ensembl.org/Homo_sapiens/Info/Index
On the search box displayed on the web page, type the RSIP number of the homozygous SNP.
A summary page will appear that provides information on the rare SNP.
In NCBI:
Details about the homozygous SNP can be obtained by searching the link http://www.ncbi.nlm.nih.gov/snp
Sift through the information contained in the SNP database to obtain details about the rare homozygous SNP.
Procedure 4: Finding the functional class
In NBCI:
Click the link http://www.ncbi.nlm.nih.gov/snp to display the SNP database on the website.
Type the gene name on the search box displayed on the page.
The search filters on the web page can generate information about the different functional classes of the gene.
In Ensembl:
Type the name of the gene on the search box located on the page.
Choose the first option – Homo sapiens – on the list of species displayed on the summary page.
On the left side of the summary page, choose the variant table.
Filter the table to derive only the information about the SNP class. This step will give you the following information.
Procedure 5:
Click genome browser link on Ensembl: http://asia.ensembl.org/Homo_sapiens/Info/Index?redirect=no
Type the name of the gene on the search box to obtain a summary page about the rare homozygous SNPs
On the left side of the summary page is the flanking sequence option. Select it.
Choose the download sequence option while focusing on the SNP variant required.
Copy and paste the sequence in a word document.
Assign the parameters 300bps before and after the SNP sequence on the word document.
Design a primer for the selected region highlighted in brown on the web page.
Set the preferred parameters in primer 3.
Assign the parameter, 600 bps, for the oligos design.
Copy the created primer information and paste it into a word document.
Works cited
Home Genome Databases copy
