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PV92 Alu Insertion (Lab Report Sample)


I was given forward and reverse DNA primers. I was expected to BLAST it over the NCBI databases, then provide answers for given questions.


PV92 Alu Insertion
It is important to note that alignment sequence was done based on the instructions given in the laboratory manual. The chosen database was denoted as "Genome (all assemblies top - level)”. This was the most preferred choice since "Genome (all assemblies top-level, Annotation Release 106)”; was not there amongst given list of choices. Thus, results differ slightly from the answers given.
Step 5
On which human chromosome did BLAST find a sequence alignment?
Answer: Chromosome 16
Homo sapiens Chromosome 16, GRCh38.p2 Primary Assembly; Sequence ID: ref|NC_000016.10| Length: 90338345, Number of Matches: 2. Hit score for the reverse primer was 49.1 bits (26), e-value was 2e-04, identities 26/26 which is equivalent to a 100% match with zero gaps introduced. The forward primer hit score was 47.3 bits (25) with an e-value of 9e-04, identities 25/25 which equivalents to a 100% match therefore, and no gaps were introduced.
Figure 1:
What is the name of the gene with which the PV92 forward primer aligns (see all headed "features”)?
The name of the gene is Cadherin 13 isoform 2. The human chromosome number 16 has high segments of duplicate nucleotide sequences. Based on Martin, et al., (2004), the chromosome contains a total of 78,884,754 base pairs as reported in the completed Human Genome Project. Manual annotation demonstrates that there are a total number of 880 protein-coding sequences, which have been verified by 1,670 transcripts alignments, 19 RNA gene sequences. It also contains 341 pseudogenes as well as 3 RNA pseudogenes (Martin, et al., 2004).
One of the genes is the cadherin gene. It encodes for calcium-dependent as well as membrane associated glyco-proteins. The uniqueness of encoded protein is that it does not have the pro-sequence as well as the tripeptide HAV binding recognition sequences which are characteristic of many types of cadherins (Martin, et al., 2004).
How good is the alignment (how many nucleotides align with the 25-long primer)?
25/25 100%, it is clear that there was no gaps which were introduced during the alignment. Thus the 25-long primer completely matched the query sequence. More information is as highlighted in Figure 2 below.

Figure 2:
What is the e-value, also called "expect," for this alignment?
2e-04 for the reverse primer and 9e-04 for the forward primer: Figure 2 above shows the query results for both.
What is the "Range" of the alignment (i.e., the numbered base-pairs, starting from one end of the chromosome) with which the forward primer sequence aligns)?
The answers given before the search are in contrary with what was determined later. The previous resu...
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