please answer all the questions Your in situ probe will need to be ~350-800 bp l

Question

please answer all the questions

Your in situ probe will need to be ~350-800 bp long. Based on your alignment of the nucleotide sequence,

1. How does ApE denote that there are direct correlation between sequences?

2. How does ApE denote that there are differences between the two sequences?

3. What does it mean when there are dashes present within the sequence alignments?

4. Are your primers identical or different? Why or why not?

5. WHY are we allowed to narrow down our search to be organism specific? Or stated another way, why don’t we have to check that our gene sequence shows up in a different organism?

6, Why would the 5’ UTR still be an “ok” region to attempt to make a distinguishing in situ probe to?

Explanation / Answer

1. ApE is a software used for sequence analysis.The correlation between two sequences in ApE is done by BLAST which finds regions of local similarities between sequences and calculates stastical significance and can be used to infer functional and evolutionary relationships between sequences.

3.In sequencing dash is used for gaps and dots are used for semi-conservative substitutions.Dash is a result of indel event (insertion/deletion of bases).

4.Primers should be Identical as only then they will bind with specific sequences and produces specific length fragments in PCR.Different primers may cause multiple binding & will produce different sizes of fragmants in PCR.

5.Narrowing down the search is needed because the ultimate goal of genome analysis is understanding the biology of organism in both functional & evolutionary terms.Same gene sequences findind in other organism is of no use because same sequence of gene in different organism may code for different protein and function too.

6.5'UTR is upstream from the coding sequence & is involved in different regulatory process.UTR sequence properties and structural features allows alternative initiation sites for translation for non AUG (start codon in m-RNA) initiation.

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