Module 3: Sequence Alignment

Due: segunda, 2 outubro 2017, 6:00

Module 3: Sequence Alignment

Objective: Use tools to sequence alignment 

Script:

Exercise 1. The genes discussed in the opening story about the Frankenstein experiment can be found in GenBank - eyeless at X79493 and human aniridia (CoreNucleotide) at AY707088. Study their local and global alignments, and discuss their statistical significance.

Obs.: Search for pairwise2. Adopt a gap penaltyto 5. Use this substitution matrix:


ATGC
A5-4-4-4
T-45-4-4
G-4-45-4
C-4-4-45

Exercise 2. Make the local alignment of the two sequences from the previous exercise. Use BLAST (bl2seq). Mention the results. 

Use the major alignmentpart of the sequence X79493 with the AY707088 to blast (nucleotide blast) against all the sequences of the GenBank database. Limit your search to nucleotide (Nucleotide collection nr/nt):

Choose Blast Nucleotide collection

In which other species this sequence part is found? This stretch is a protein domain or have another biological significance?

Obs.: http://www.ncbi.nlm.nih.gov/blast. -> nucleotide blast Link

Exercise 3. Protein-codingDNAsequences are best aligned after translation into amino acids. Find 2 homologous genes in HomoloGene database, for exemple ssh (SonicHedgeHog) or p59, and verify if it occurs (align them both as nucleotide sequences, and then as amino acid sequences.).

Obs.: To make the alignment use the blastn and the tblastx. Blastn compares a nucleotide sequence against another nucleotude sequence. tBlastx compares a translated nucleotide sequence against another translated nucleotide sequence.

Exercício 4. Make the multiple alignment of the human sequenceAAH07284), sheep sequence(AAX39333) and cow sequence (AAP41546) using the CLUSTALW. Comment the results

Obs.: Possible web server to the clustalwhttp://www.ebi.ac.uk/Tools/clustalw2/.

Good work!