NCBI BLAST: Extra Exercises Part 1: Identifying Sequences

Open NCBI BLAST

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

This is an extra exercise to practice using NCBI BLAST.

Remember that BLAST allows you to input a sequence from DNA, RNA or protein residues (amino acids) and find sequences that are identical or similar.

Let's identify a nucleotide sequence.

You can get to BLAST directly by going to http://blast.ncbi.nlm.nih.gov/

For the first part of this exercise we will give you a nucleotide sequence to identify. Click Nucleotide BLAST on the left of the page.

Link to Nucleotide BLAST

Copy and paste the entire string of nucleotide symbols, below, into the box under "Enter Query Sequence."

Copy this:

>Seq1
ATGGGTAAGGAGGACAAGACTCACCTTAACGT
CGTCGTCATCGGCCACGTCGACTCTGGCAAGT
CGACCACTGTAAGTACAACCAACAGCGGGTTG
CTTATCTGCACTCGGAATCCGCCAAACCTGGC
AGGGTATCACCAAAACATCTTGCTAACTTTTG
ACAGACCGGTCACTTGATCTACCAGTGCGGTG
GTATCGACAAGCGAACCATCGAGAAGTTCGAG
AAGGTTAGTCAATATCCCTTCGATTACGCGCG
CTCCCATCGATTCCCACGATTCGCTCCCTCAC
TCGAAACACATCCATTACCCCGCTCGAGTCCG
AAAATTTTGCGGTGCGACCGTGATTTTTTCTG
GTGGGGTATCTTACCCCGCCACTCGAGTCACG
GATGCGCTTGCCCTGTTCCCACAAAACCTTAC
CACCCTGTCGCGCACTACATGTCTTGCAGTCA
CTAACCACTGGACAATAGGAAGCCGCCGAGCT
CGGAAAGGGTTCCTTCAAGTACGCCTGGGTTC
TTGACAAGCTCAAAGCCGAGCGTGAGCGTGGT
ATCACCATTGATATCGCTCTCTGGAAGTTCGA
GACTCCTCGCTACTATGTCACCGTCATTGGTA
TGTTGTCACCGTCTCACACTATCATGTATTCA
TCATGCTAACATCTCTCTCAGATGCCCCCGGT
CATCGTGATTTCATCAAGAACATGATC

to here:

standard blast page

Uncheck this box labeled "Align two more sequences:"

A screenshot showing the "Align two or more sequences" checkbox.

then scroll down and click the BLAST button:

blast button

[Long page -- please scroll down]

Once your results are displayed, you will see a header followed by the results of your search. The results can be displayed in several different views, including a list of sequence "Descriptions," via a "Graphic Summary," and via a more detailed "Alignments" view.

 BLAST alignment page options

Click on the Descriptions tab (if you're not there, already) to learn more about each of the sequences that aligned with yours.

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

 linked from description to alignment

Note that your list will be different from this screenshot, but the top results should still be the same organism and gene/protein.

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Click on the Sequence ID to view the full record and learn more about the sequence.

click on sequence ID

What organism is this sequence from?

What gene is this sequence from?

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Now go back to the Nucleotide BLAST (BLASTn) homepage and BLAST this sequence:

>Seq2
ATGGGAAAGGAGAAGACCCACATCAACATCGTTGT
CATTGGGCACGTAGATTCAGGGAAGTCTACCACGA
CTGGCCATCTGATCTATAAATGTGGCGGGATCGAC
AAGAGAACAATTGAAAAGTTCGAGAAGGAGGCTGC
CGAGATGGGAAAGGGCTCCTTCAAATATGCCTGGG
TCTTGGACAAACTTAAAGCTGAACGTGAGCGTGGT
ATCACCATTGATATCTCCCTGTGGAAATTTGAGAC
CAGCAAGTACTATGTTACCATCATTGATGCCCCAG
GACACAGAGACTTCATCAAAAACATGATTACAGGC
ACATCCCAGGCTGACTGTGCTGTCCTGATCGTTGC
TGCTGGTGTTGGTGAATTTGAAGCCGGTATCTCCA
AGAACGGGCAGACCCGTGAGCATGCCCTTTTGGCT
TACACCCTGGGTGTGAAACAACTAATTGTTGGCGT
TAACAAAATGGATTCCACTGAGCCACCCTATAGCC
AGAAGAGATACGAAGAAATTGTTAAGGAAGTCAGC
ACCTATATTAAGAAAATTGGCTACAACCCCGACAC
AGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTG
ACAACATGCTAGAACCAAGTGCTAATATGCCATGG
TTCAAGGGATGGAAAGTCACCCGTAAGGACGGCAA
TGCCAGTGGAACCACCCTGCTTGAAGCTCTGGATT
GCATTCTGCCACCAACTCGCCCAACTGACAAACCC
TTGCGTTTGCCTCTCCAGGATGTCTATAAAATTGG
TGGTATTGGTACTGTCCCTGTGGGTCGTGTGGAGA
CTGGTGTTCTCAAACCTGGCATGGTGGTCACCTTT
GCTCCAGTCAATGTAACAACTGAAGTGAAGTCTGT
AGAAATGCACCATGAAGCATTGAGTGAAGCCCTTC
CTGGGGACAATGTGGGCTTTAATGTCAAAAACGTG
TCTGTCAAAGATGTCCGTCGTGGCAATGTGGCTGG
TGACAGCAAAAATGATCCACCCATGGAAGCTGCTG
GCTTCACAGCTCAGGTGATTATTTTGAACCATCCA
GGCCAAATCAGTGCTGGATATGCACCTGTGCTGGA
TTGTCACACAGCTCACATTGCTTGCAAGTTTGCTG
AGCTGAAGGAGAAGATTGATCGTCGTTCTGGGAAA
AAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGG
TGACGCTGCCATCGTTGATATGGTTCCTGGCAAGC
CCATGTGTGTCGAGAGCTTCTCTGATTATCCTCCC
CTGGGCCGTTTTGCTGTGCGTGACATGAGACAGAC
AGTCGCTGTGGGTGTCATCAAAGCAGTGGACAAGA
AGGCAGCTGGAGCTGGCAAGGTCACCAAGTCTGCC
CAGAAAGCTCAGAAGGCTAAATGA

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What organism is this sequence from?

What gene is this sequence from?

You just found two translation elongation factor 1-alpha sequences from two different species.

In part 2, we'll compare these two sequences to find the similarities.

Continue to NCBI BLAST Extra Exercises Part 2: Algorithm Sensitivity

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