CPGR Workshop â Tutorials Tutorial 1 â Evaluating loci to be ...

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10. Now that we have the sequence of the locus in FASTA format, we can use

the NCBI BLAST server to search the locus against all the Xanthomonas

sequences in GenBank. Go back to the CPGR Workshop Links page and open

the NCBI BLAST Page in the browser. To begin, paste the sequence in the text

box. The locus sequence is the query sequence and will be used to search

against the database of non-redundant GenBank sequences. The sequences in

the database are also known as the subject.

11. Searching against the entire non-redundant GenBank set of sequences is too

wide in this case as we want to limit the search to all of the Xanthomonas

sequences in GenBank. To do this, scroll down to the Choose Search Set panel

and choose the ‘Others’ Database option. Next, select the ‘Custom’ option for the

Organism. Start typing Xanthomonas in the text box. As you type, a drop drown

box will appear showing the available options as your typing narrows them down.

When you see Xanathomonas (taxid:338) appear, select it.

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8. You should now have the nucleotide sequence of the locus in FASTA format displayed in the browser. 9. When doing a bioinformatics analysis, it is useful to keep of log of downloaded sequences, results, and output in a text editor. This prevents losing work if a browser crashes or you want to save your work. To do this, open notepad in windows (Start -> Run – type notepad in the “Open:” box). The FASTA sequence can be copied and pasted straight from the browser into notepad.

10. Now that we have the sequence of the locus in FASTA format, we can use the NCBI BLAST server to search the locus against all the Xanthomonas sequences in GenBank. Go back to the CPGR Workshop Links page and open the NCBI BLAST Page in the browser. To begin, paste the sequence in the text box. The locus sequence is the query sequence and will be used to search against the database of non-redundant GenBank sequences. The sequences in the database are also known as the subject. 11. Searching against the entire non-redundant GenBank set of sequences is too wide in this case as we want to limit the search to all of the Xanthomonas sequences in GenBank. To do this, scroll down to the Choose Search Set panel and choose the ‘Others’ Database option. Next, select the ‘Custom’ option for the Organism. Start typing Xanthomonas in the text box. As you type, a drop drown box will appear showing the available options as your typing narrows them down. When you see Xanathomonas (taxid:338) appear, select it.

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Page 3: 6. Now you have a GenBank record fo
Page 7: 14. Click the large ‘BLAST’ but

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