Human DNA BLAST Results
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By now you should have the BLAST results back and open in another window.
We will now look at the results. The general layout, and the way the data is displayed should now be fairly familiar to you. However, we will:
  1. look at the different results sections
  2. examine the graph
  3. look at the sequence table
  4. look at, and interpret the alignment
The BLAST images below are taken from a search run on Sunday October 14, 2018 at 1:47:12 pm.
The Human DNA BLAST results - page header
The page header is always worth a glance if only to make sure you ran the right program and the right database was searched.
Top of the BLAST result page
1) What is the length of the DNA used for the search?
One answer only.
   2386
   3246
   3268
   3286
   3296
   4255
   4386
The Human DNA BLAST results - the graph
The graph gives an overview of the results returned and an indication of the degree of match. Moving your mouse over the graph will show the name of the DNA.
The BLAST graph - the graph shows the degree of match between your sequence and sequences in the database. In the case above you can see the matching transcript - the top line, and also the chromosomal location and intron/exon relationships.
The Human DNA BLAST results - the table
The BLAST table - the table shows the matches along with links to the full database entry and alignment. The top hit is the best match. The table is divided into transcripts and genomic data.
The BLAST table shows the hits ordered by best to worse.
1) In the above figure (not your results) what is the accession number of the top genomic sequence?
One answer only.
   MT_029419
   NC_000012
   NC_018923
   NT_029491
   NC_018932
   NT_229419
   NT_229410
   NM_015292
2) The E value of 0.0 for the first sequence in the above table shows that
One answer only.
   it is a very poor match.
   the DNA has not been fully sequenced.
   the DNA is unique in the database.
   there are no mismatches.
   it is a good hit.
   all mismatches are conserved.
The Human DNA BLAST results - the alignment
The alignment must be examined. Just because a DNA is listed in the table, it does not mean it is a good match.
The easiest way to navigate to the alignments is by clicking on the link in the table.
  1. Click on the link for the top transcript alignment.
Clicking on the link - the sequence description - will take you to the alignment
The first alignment shows a very good match. This is not surprising as it is a transcript.
This is part of the top DNA alignment for a search run on the date shown at the top of the page. Note that this is an exact match. The identities score is 100%, and and that there are no gaps.
  1. Now click on the top link in the table for Genomic Sequences (Homo sapiens chromosome 12, GRCh38.p12 Primary Assembly) to take you to the first genomic match.
The above figure shows the first alignment in the genomic section of the results
1) Is the above sequence alignment a good match?
One answer only.
   Yes
   No
   Yes and no
2) Why are you seeing a series of short localised matches in the genomic data, and opposed to the long match seen for the transcripts (you may need to scroll down on the search page to see the other alignments)?
One answer only.
   presence of introns and exons in the genomic data means that a full match will not be acheived
   the sequence you used to search is incomplete
   the sequence you used for search contained only introns
3) Were any gaps inserted to get the local alignment in the above figure?
One answer only.
   No
   Yes
So far we have:
  1. carried out a Human DNA BLAST search
  2. looked at the returned results
  3. examined the sequence alignments
From these results, it is possible to look at the location and mapping to the human genome, but this is beyond the scope of this practical.
Next, we will look at searching the sequence databases with short peptide and DNA sequences.
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