Exercise #2: Get BLAST results in a genomic context
Background
Many of us like to see our BLAST alignments in the context of a gene or chromosome.
Some BLAST results contain direct links into GDV, the Genome Data Viewer.
You will learn which BLAST databases to search to get these links.
In Option #3, we'll see the effect of setting a smaller word size.
Setup
Use the same query as in Exercise #1, or retrieve RID KNWN00VF016
Option #1
Select the database, RefSeq Representative genomes, and limit to human (taxid:9606)
Click here to see the RID
RID for the RefSeq Representative genomes search: M3T18F9J013
Option #2
Use the "BLAST Genomes" section of the BLAST home page, and limit to human (taxid:9606).
Click here to see the RID
RID for the human genome search: KVCHCGGS013
Option #3
Run blastn, not megablast, to see the effect of a shorter word size.
Click here to see the RID
RID for the human genome search, blastn rather than megablast: KVAAC90V013
Take-away Message
- To see your BLAST alignments in the Genome Data Viewer, search a database with chromosome-level sequences. Most often, those sequences are RefSeq genomic records (NC_*), but could be GenBank records (no underscore in the accession number).
- What is the best BLAST database for searching genomic records? If you want to search just one organism, start with the "BLAST genomes" section on the BLAST home page. Otherwise, run nucleotide BLAST against the "RefSeq Representative genomes" database.
- For a more sensitive search, run blastn rather than megablast. The primary difference between these programs is a smaller, default word size.
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Last Reviewed: October 8, 2022