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Exercise 3: Why do I get no hits?


Background

BLAST page message, No significant similarity found.

Sometimes your BLAST search gives you this message, "No significant similarity found".
We'll try some ways to address that.

Setup

Retrieve the results for RID: KVFM4C5G013

Click here if the RID has expired

Use these settings to run a new search:

    • Query:  ~1kb from Carcharodon carcharias (great white shark)
TTTTCACTTAACTTTGTACCATTAGCAAACTTTTGGCCTCTTTGTCTAAATCATTAATATAGACTGTAAGTAGCTGAGGCCCCAGCGCTGATCCTTCAGCACCTCACCTGCTAACTTGAAAATGCCCATTTATCCCTATTCTCTTCTTCCTGTTTGTTAACCAATCCTCTATCCATGTTAATGTATTATCCCCACCTCCATCTTAACTTGCATATCAACCTTTTTATGTAGCACCCTATCAAAAGCCTTTTGGAAATCCAAGTACACTACATCTATGGTAACCCTTTACCGACTCTAGTAGTTACATCCTCAAAAAGTTCTAATAAATCTGTCAAACATAATTTTCTTCTCATAAAACCATATTGACTTTGTCTGATAAAAATGATTTTCTAAGTGAATTGTTAATAATTCATTAAGAATAAGTTCCAGTATTTTCCCAATGACTGGCCCAGGCTAACAGGCCTGTAAGTTCCCTGCTTTCTCTCTCCCTCCTTTCTTGATTGGTGATGTAACATTACTAACTTCCAATCTGCTGAGACCATTTTGGAATCCAGGAAAATTTGGAAAAATCATAACCAGTGCAGTTAAAAAATAGGTCTTTTTTTCTGTATTGACCCAGCCATTTGATCATTTAATTTGCTTTAGGTTGGTCAAAGCCAATATTGAATATTTAAATTCACTAACAAATGAAGGGAAGAGGACAAAAAGCAAGTTTTTGACAAGGAATAGGGCAAAAATGCAAAATGCTGGCATTATTAGTGCATGTTGTTCCATTTTTTGTTGGCAGCTAGTGAACCTAAGAGTGATACTATAACATAGTACGGAGAAAACCTTCAGTCCATCAATCTTGCATTTTCTTGGTGCATTTCTAATAAGGTTGAATCCCAAATGTTGGCAAGAACCCATTTTGTTGCTTCTTGAAACCCATTAGAGTTTCTCGTCCACCAAACATGCCACAGACGTGTTCAGCATATTTGCCACACTTT
    • Database: nt
    • Organism: Carcharodon carcharias (taxid:13397)

Option #1

Change the database to WGS.

Click here to see the RID

RID for the wgs search: KH01AEZ2016


Option #2

Another database option is the Carcharodon carcharias (great white shark) genome BLAST page, which will provide the genomic context. Start with the "BLAST Genomes" section of the BLAST home page, and select Carcharodon carcharias (taxid:13397).

Click here to see the RID

RID for the BLAST Genomes search: KPB37W15013


What if my BLAST alignments have no link to GDV?

In our last search, RID KPB37W15013, the alignment to NC_054478.1 has no link to GDV.
You can still view the BLAST alignment in our Sequence Viewer. Here are two ways:

  1. Use the "Graphics" link in the Alignment view of the BLAST results.
  2. Use the BLAST widget in GDV to add the RID number, as shown below.

BLAST widget in GDV

Take-away Messages

To address the message, "No significant similarity found", try:
  • Searching a different database
  • Changing to the blastn program, or decrease the word size
  • Increasing the Expect threshold
If your alignment to a genomic, NC_ record has no link to the GDV, you can use the "Graphics" link in the Alignment view, or add the RID within the GDV.

Last Reviewed: October 8, 2022