NCBI BLAST (Part 2): Exploring Your BLAST Results

Open BLAST Results

in another browser window to work through this tutorial side by side.

Exploring your BLAST Results

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You should be viewing your BLAST results from Part 1 in your other browser window.

Click on the Descriptions tab to learn more about each of the sequences that aligned with yours.

Click on the description of the sequence to see the alignment.

For this exercise, select one of the sequences labeled, "Homo sapiens haplogroup...mitochondrion, complete genome."

sequence description links

Clicking on a sequence will bring you to the Alignments view.

Exploring your BLAST Results

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You can now see all the nucleotide base matches between your sequence (the "query" sequence) and the sequence from the database (the "subject" sequence).

H3i haplogroup

This particular alignment isn't very interesting to look at because the two sequences match perfectly. In the next example we'll look at two sequences that do not perfectly align so that you can look at differences.

Our goal right now is simply to identify the sequence and explore the results.

What chromosome is the subject ("Sbjct") sequence (this one on the database that matched your query) from?

The first base in your query ("Query") sequence aligns with approximately which base in the Subject ("Sbjct") sequence?

Exploring your BLAST Results

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To go to the subject sequence in the Nucleotide database, there are several links from the alignment.

links to nucleotide

The first two: (1) one in the header next to Download labeled GenBank, and (2) another link from the Sequence ID, take you to the record for the full sequence as it was submitted (or created). Remember that our match starts around base 7586. The third link (3), adjacent to the range (also labeled GenBank), takes you to a record displaying just the range of interest (around 7586 to 8269).

Either record might be useful, but let's look at the record for the entire sequence that was submitted, and look at our query sequence in that context.

Follow the link to the GenBank record in the Nucleotide database from your Sequence ID (OK266950.1 in this example):

link from sequence ID

[If this page insists on opening in a new browser tab, you can use this link instead to go to OK266950.1]

Exploring your BLAST Results

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You should now be in the NCBI Nucleotide database, looking at a record labeled something like, "Homo sapiens haplogroup H3i mitochondrion, complete genome." (You may be looking at a different haplogroup record.)

What is a haplogroup?

Many of the records we look at in this course are Reference Sequences or "RefSeq" records, which are curated by NCBI. But this is an "original" sequence record submitted by a GenBank participant.

Approximately how many bases does this record include?

In what section of the record can you find the name of the affiliation of the researcher or organization that submitted the record?

Exploring your BLAST Results

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An interesting part of a Nucleotide record is the section labeled "FEATURES." Called the "feature table," this is the part that reflects scientists' annotations -- notes on what biological features of interest are known about a sequence.

Scroll down the feature table of this mitochondrial DNA record. Definitions of some of the feature labels can be found in the GenBank Sample Record.

Two features of major interest include:

  • CDS = a coding sequence, or region of nucleotides that corresponds with amino acids in a protein.
  • gene = a region identified as a gene. A gene may include multiple sections of coding sequences, so the same nucleotide sequence (shown in a number range) may be labeled as CDS and gene.

In the feature table, each labeled feature is hyperlinked to the sequence itself, which is at the bottom of the record. Click on the first instance of a "gene" label in this feature table.

gene link from feature table

You can now see the sequence for the gene highlighted in the context of the rest of the sequence:

ND1 sequence

Exploring your BLAST Results

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The tools that appear at the bottom provide a useful way to learn and navigate your way around the features.

For example, since you clicked on a gene, you can now toggle through all the genes in this record using the tool in the lower left.

toggling between features in a Nucleotide record

How many genes have been labeled in this human mitochondrial DNA record?

Click around this feature table for a few minutes to get more accustomed to looking at this data.

When you're ready, move on to NCBI BLAST (Part 3): Compare Sequences to explore these mitochondrial sequences in an interesting way using BLAST.

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