BLAST Exercise: Detecting and Interpreting Genetic Homology

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Interpreting the blastx Output: Figure 8. Initial list of blastx hits to our sequence If you emulated our analysis thus far, you should now have strong blastx hits to the Swallow protein (Figure 8). However, remember that sequence similarity does not necessarily imply that our sequence contains the D. melanogaster version of the Swallow protein. We need to gather more evidence before deciding how to annotate our sequence. First, we need to find out more about the Swallow protein. A good place to start is the Swissprot database, which is hand-curated and has links to many other databases. To access the information for a protein, you need its Swissprot accession string, which is found in the last part of the GenBank accession number. In this case, we would like to examine the protein (SWA_DROME) that produces the most significant alignment (5e-148) with our sequence. A Swissprot accession string consists of an abbreviated gene name, followed by an abbreviation indicating which organism the particular protein in this entry came from. For example, SWA_DROME means that the abbreviated gene name is SWA and the source of the protein is DROsophila MElanogaster. Figure 9. The Expasy web site contains information on the sequences curated in the Swissprot database 8
Figure 10. Results when searching for “Swallow” in the Expasy web site To access a Swissprot entry by its accession string, go to the Expasy web site (http://us.expasy.org) and enter the accession string in the search dialog box at the top of the page (Figure 9). You can also do a keyword search, such as “Swallow,” to find multiple entries (Figure 10). Alternatively, the record for SWA_DROME is also available in the tutorial package (file named SwissProtEntry.html). Figure 11. Swissprot entry for the Swallow Protein Question 6: Based on the Swissprot entry (Figure 10), what does Swallow do Does your blastx output match Swallow genes from more than one species, and if so, which species If you want to talk about this gene in your own work, whom should you cite as having discovered it (Hint: look at the GenBank record by clicking on the accession number, gi|xxx) Now that we know a bit more about the candidate matches to our gene, let’s take a closer look at the blastx output. To produce an annotation, we need to verify that the query sequence really does contain the D. melanogaster Swallow gene. In particular, the match should be full-length, including all the coding exons of the gene. If exons are missing, this may indicate a pseudogene. To look at the alignment, go back to the blastx output page and click on the score. 9
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Page 3 and 4: Figure 1. RepeatMasker Web Server a
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BLAST Exercise: Detecting and Interpreting Genetic Homology

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