Lab Exercise $-$ Practical $8-$ part $1$

By using a manually generated dot plot, align the provided sequences and calculate their scores accordingly:

a$)$ Sequence A: TCAACTGAGTTCTGTTTAATG Sequence B: TCGACAGGGTTTTGCTTAATG

b$)$ Sequence C: TCAACTAGTTCTGGTAAGGATTGAG

Sequence D: TCGACTACAGTACTGCGTAAGTTGAG

Scoring scheme:

Match $=+2$

Mismatch $=-1$

Opening gap $=-2$

Gap extension $=-1$

No penalty for terminal gap

Include the generated dot plot, manual alignment and scoring calculation in the lab report.

Lab Exercise $-$ Practical $8-$ part $1$

$2.$ By utilising the accession ID provided below, answer the following questions accordingly:

$1.N{P}_{000508\mathrm{.}1}$

$2.N{P}_{494883\mathrm{.}1}$

a$)$ On which database the sequences are stored?

b$)$ Identify the sequence type and provide a brief information regarding each of the sequence

c$)$ Explore, identify and briefly list out the steps on how to obtain and download the sequence $($FASTA format$)$ for both of the provided IDs

d$)$ By using the downloaded sequences, conduct PSA using appropriate EMBOSS programs for:

i$.$ Local alignment

ii$.$ Global alignment

Obtain a snapshot of the obtained results and briefly compare them, plus, include the name of the corresponding programs used to obtain the result of the alignments