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Answer to Question #59570 in Bioinformatics for Jazz

Question #59570
Biological Sequence alignment.
a) Calculate the alignment score for different alignments and indicate the best possible
aligned sequence for the following sequence:
ACCTAGCTAGCCGAT
ACCCCTAGGCGAAA
Use Match: +1, Mismatch:-1 and Indel: -2
i. Show all possible alignments and their scores
ii. Which is the best possible alignment? State the reason.
b) Carry out a Multiple Sequence Alignment (MSA) for the protein Ras 1. Use the UniProt
(http://www.uniprot.org/) database for retrieving the protein sequence of keratin type2.
The protein sequences from the following organisms must be included in your MSA.
1) Homo sapiens (Human)
2) Drosophila melanogaster (Fruit Fly)
3) Candida albicans (Yeast)
4) Mus musculus (Mouse)
5) Gallus gallus (Chicken)
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