Alignment and Phylogeny Exercises

1. Align these two sequences:

AACTCCTGGACTCAAGTGATCCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAG

AACTCCTGGGCTGAAGCGATCCTATCCTCTTGCCCTCTCGAAGTGCTGAGATTACCA

2. Use BLAST to search human genome.
Use "Nucleotide Sequence."
Search "Reference Genomic Sequences."
Use "More dissimilar" option. What sequence feature is this?
Perform "Distance tree."

ctcactctgt tttccaggct ggcctcaaac ttgaactcct ggactcaagt gatcctcctg
cctcagcctc ccaagtagct gggattacag gcttgtgcca cagcactgga ccaatatata

3. BLAST search "Proteins" for the POMC precursor. Are there conserved domains?
Explain what they are. Why are there more than one? Make a distance tree.
Which kind of organisms have POMC?

1 csrsgallla lllqasmevr gwclessqcq dlttesnlle cirackpdls aetpmfpgng

61 deqpltenpr kyvmghfrwd rfgrrnssss gssgagqkre dvsagedcgp lpeggpeprs

121 dgakpgpreg krsysmehfr wgkpvgkkrr pvkvypngae desaeafple fkreltgqrl

181 regdgpdgpa ddgagaqadl ehsllvaaek kdegpyrmeh frwgsppkdk ryggfmtsek

241 sqtplvtlfk naiiknaykk ge

4. BLAST search Npe2. Use "More dissimilar sequences" option.

ACTAATGCGCGCATTAGTGGATAAAAGCAGTCTCAAGGGTCTCTTCACGAGGTC

5. BLAST search NR for this unknown sequence. What is it? Make a distance tree. What kind of organisms have it? How does it relate to what other organisms have?

1 vpmdcsrypn ttseegkvmi lcnkalnpvc gtdgvtydne cvlcahnleq gtsvgkkhdg

61 ec