Introduction to UCSC Genome Browser (Tutorial) PDF

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

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UCSC GENOME BROWSER Database link: https://genome.ucsc.edu/ Purpose: Browse & visualize human genome through interactive Genome Browser, align sequences to the genome using BLAT, retrieve data from Table Browser by applying constraints, find amplicons in the genome using In-silico PCR and find similar genes within a genome using GeneSorter.

Introduction: UCSC Genome Browser is a Genome Database that presents sequence data and its annotations in a graphical manner or through a graphical browser. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website. The homepage of UCSC is shown in the Figure 2.1

Figure 2.1 The homepage of UCSC

Steps: ● I visited the homepage of UCSC via the link: https://genome.ucsc.edu/ ● Open BLAT from the Tools provided on the homepage of UCSC. ● Selected genome, assembly query type (Base DNA, protein) and BLAST guess Output (ace to query score) and output type (hyperlink). ● Opened the Genome browser again in the new tab. Clicked tools and opened the table browser Clade (Mammal), genome (human) Assembly group (gene & gene prediction) region (mif) and clicked on “look up”. ● List showed I clicked on one of them to analyze that entry. ● When the homepage of UCSC genome browser opened, I clicked on ‘genome browser’. When the homepage of ‘genome browser’ opened, I wrote the gene name BDNF and selected the recent search and entered. Results opened up. Figure 2.2 ● After interpreting these results, I went to ‘table browser’ and selected clade ‘mammal’, genome ‘humans’, recent assembly group 'mapping and sequencing’ and then wrote the gene name at position portion, then hit up the ‘lookup’ button. Figure 2.3 ● All genecode genes appeared on screen, I selected the 2nd option/link from the results and the position of the query gene appeared in the position box, from which I clicked on ‘get/output’ for results. ● After that I chose the filter and submitted it and again clicked on ‘summary/statistics/ button to get the results. ● Then I went to in silico PCR from the homepage of UCSC genome browser, then typed in the forward primer and clicked on ‘go’ to get the in silico results. Figure 2.4 ● Then I went to the gene sorter and typed in the name of the gene and clicked on the sort by, after that again I gave the gene name and clicked on “GO”. ● Then I visited the homepage of UCSC and clicked on ‘DNA Duster’ from the “Tools” option. ● I pasted the sequence for clearing any gap between nucleotides and submitted to get the results which I then analyzed.

Figure 2.2: Genome Browser on UCSC for Human GRCh38/hg38

Figure 2.3: Table Browser

Figure 2.4: In Silico PCR Results...