4.1. Access the internet and log on to the UCSC Genome Bioinformatics Web Page (Figure 1-

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1 1. PURPOSE To provide instructions for finding rs Numbers (SNP database ID numbers) and increasing sequence length by utilizing the UCSC Genome Bioinformatics Database. 2. MATERIALS 2.1. Sequence Information for SNPs of interest 3. ATTACHMENTS 3.1. N/A 4. PROTOCOL 4.1. Access the internet and log on to the UCSC Genome Bioinformatics Web Page (Figure 1- Figure 1-UCSC Genome Bioinformatics Home Page 4.2. Click on Blat Search and the following screen will appear:

2 Figure 2-Blat Search Page 4.3. Copy and paste the sequence of interest into the window as shown below: Figure 3-Entering Sequence for Blat Search

3 If applicable, delete the brackets from around the SNP site. Delete one of the SNP bases and the slash while leaving the other SNP base in the sequence Click Submit, and the following page will appear if the database recognizes the sequence: Figure 4-Blat Search Results 4.5. The Results page gives the option of selecting Browser or Details, while also providing a score, Qsize, identity percentage, chromosome number, strand, the start and end point of the sequence within the chromosome Clicking Details will show the cdna and genomic DNA sequence as shown in the following figure:

4 Figure 5- Details of a Blat Search 4.6. Click Back return to the Blat Search Results page. (Note: If you receive a message that the Website has expired, click Back again and resubmit your sequence from the Blat Search Genome page Clicking Browser will yield the following page: Figure 6a, 6b- Browser Information following a Blat Search

5 Finding rs numbers On the Browser information page, click on Single Nucleotide Polymorphisms (SNPs) from Clone Overlaps or Single Nucleotide Polymorphisms (SNPs) from Random Repeats. This will display the individual rs numbers of the SNPs located in the submitted sequence Click on one of the rs numbers listed under the Single Nucleotide Polymorphism (SNPs) categories and the following screen will appear.

6 Figure 7-Single Nucleotide Polymorphism rs Page Check the sequence on the screen against the sequence surrounding the SNP that you are interested in. If the sequences match, you have found the correct rs number. If not, click back to return to the previous page and continue clicking on the remaining rs numbers until you have found the SNP of interest Additional information about the SNP of interest can be gathered by clicking the dbsnp link at the bottom of this page. Clicking this link will bring you to an NCBI SNP webpage shown below.

7 Figure 8-NCBI Database Single Nucleotide Polymorphism Page Increasing Sequence Return to the UCSC Genome Browser Page (See Step 4.6.1). Click DNA on the top of the UCSC Genome Browser page and the following screen will appear. Figure 9-Get DNA Window

8 Type the number of extra bases you would like added upstream and downstream of the sequence you have submitted in the spaces provided Click Get DNA and the following screen will appear. Figure 10-DNA Sequence Information The sequence can be copied and pasted into documents in Microsoft Word, Microsoft Excel, Notepad, etc. NOTE: You can also use this method of extension to mask the repeat sequences to N. Under the Sequence Formatting Options, select the circle adjacent to Mask repeats to N. There are other formatting options available in this section and by clicking the Extended Case/Color Options button When you are finished, click on the X in the corner of the window to close the program.