Question

Use the PopSet (population study data sets) in ENTREZ to retrieve coding sequence (CDS) of amylase-related gene (amyrel) generated for Drosophila yakuba by Cariou et al. (2001). You should retrieve 5 Drosophila yakuba sequences from different population strains. ***Make sure all your sequences are Drosophila yakuba.***

(a) Report the GenBank accession numbers.

(b) Align coding regions of the 5 sequences. Which alignment software did you use?

(c) Look at the first 200 bases of the alignment. Count the numbers of segregating sites(K), the numbers of segregating sites per sites (k), and nucleotide diversity (π).

Answer 1

Go to the site https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html and select ENTREZ

https://www.ncbi.nlm.nih.gov/gquery/ and select PopSet

Enter amyrel in the search column

https://www.ncbi.nlm.nih.gov/popset/12620152 - this has Cariou et al (2001) amyrel sequences for different strains of Drosophila yakuba

(a)

1) GenBank: AF280878.1 : Drosophila yakuba strain LO4

2) GenBank: AF280877.1 : Drosophila yakuba strain LBV2 clone 4

3) GenBank: AF280876.1 : Drosophila yakuba strain LBV2 clone 1

4) GenBank: AF280875.1 : Drosophila yakuba strain SA3 clone 8

5) GenBank: AF280874.1 : Drosophila yakuba strain SA3 clone 6

b) Get the FASTA sequence of each strain and use Multiple sequence alignment -Clustal Omega

https://www.ebi.ac.uk/Tools/msa/clustalo/

Results :

CLUSTAL O(1.2.4) multiple sequence alignment


AF280878.1      ATGTTCAAGTTGGCTTTGACCCTGACACTCTGCTTGGCGGGCAGCCTCTCGCTGGCCCAG    60
AF280876.1      ATGTTCAAGTTGGCTTTGACCCTGACACTCTGCTTGGCGGGCAGCCTCTCGCTGGCCCAG    60
AF280877.1      ATGTTCAAGTTGGCTTTGACCCTGACACTCTGCTTGGCGGGCAGCCTCTCGCTGGCCCAG    60
AF280875.1      ATGTTCAAGTTGGCTTTGACCCTGACACTCTGCTTGGCGGGCAGCCTCTCGCTGGCCCAG    60
AF280874.1      ATGTTCAAGTTGGCTTTGACCCTGACACTCTGCTTGGCGGGCAGCCTCTCGCTGGCCCAG    60
                ************************************************************

AF280878.1      CACAATCCCCATTGGTGGGGCAATCGCAACACCATCGTCCACTTGTTCGAGTGGAAGTGG    120
AF280876.1      CACAATCCCCATTGGTGGGGCAATCGCAACACCATCGTCCACTTGTTCGAGTGGAAGTGG    120
AF280877.1      CACAATCCCCATTGGTGGGGCAATCGCAACACCATCGTCCACTTGTTCGAGTGGAAGTGG    120
AF280875.1      CACAATCCCCATTGGTGGGGCAATCGAAACACCATCGTCCACTTGTTCGAGTGGAAGTGG    120
AF280874.1      CACAATCCCCATTGGTGGGGCAATCGAAACACCATCGTCCACTTGTTCGAGTGGAAGTGG    120
                ************************** *********************************

AF280878.1      TCGGACATTGCCCAGGAGTGTGAGAATTTTCTGGGACCCCGAGGATTCGCCGGCGTTCAA    180
AF280876.1      TCGGACATCGCCCAGGAGTGTGAGAATTTTCTGGGCCCACGAGGATTCGGCGGCGTTCAA    180
AF280877.1      TCGGACATTGCCCAGGAGTGTGAGAATTTTCTGGGACCCCGAGGATTCGCCGGCGTTCAA    180
AF280875.1      TCGGACATCGCCCAGGAGTGTGAGAATTTTCTGGGCCCACGAGGATTCGCCGGCGTTCAA    180
AF280874.1      TCGGACATCGCCCAGGAGTGCGAGAATTTTCTGGGCCCACGAGGATTCGCCGGCGTTCAA    180
                ******** *********** ************** ** ********** **********

AF280878.1      GTGAGCCCCGTGAATGAGAACATCATATCGGCGGGTCGTCCTTGGTGGGAGCGATACCAA    240
AF280876.1      GTGAGCCCCGTGAATGAGAACATCATAGCGGCGGGTCGTCCTTGGTGGGAGCGATACCAA    240
AF280877.1      GTGAGCCCCGTGAATGAGAACATCATAGCGGCGGGTCGTCCTTGGTGGGAGCGATACCAA    240
AF280875.1      GTGAGCCCCGTGAATGAGAACATCATAGCGGCGGGTCGTCCTTGGTGGGAGCGATACCAA    240
AF280874.1      GTGAGCCCCGTGAATGAGAACATCATAGCGGCGGGTCGTCCTTGGTGGGAGCGATACCAA    240
                *************************** ********************************