Sonja Harrower
Table of Contents

Week 2


Using the Blast function within the NCBI website five homologous sequences of the H.sapien alcohol dehydrogenase 7(ADH7) were found. The alcohol dehydrogenase family of enzymes is responsible for metabolizing alcohols within organisms. ADH7 differs from others in this oxidoreductase family in that it is more highly expressed in the stomach rather than the liver and is inefficient at processing ethanol (ADH7, 2011). Amino acid sequence and nucleic acid sequences of ADH7 were downloaded for R.norvegicus (brown rat), M.musculus (house mouse), M.mulatta (Rhesus macaque), B.taurus (cattle) and P.abelli (Sumatran orangutan).
The ClustalW_P function within Swami workbench was used to align the amino acid sequences twice with different gap opening and extension penalties. Even with gap penalties differing by 10 fold there was no difference in the alignments produced by the program. There was no greater alignment to be achieved with more or longer gaps.
From this initial alignment the two most closely related amino acid sequences, B.taurus and R.norvegicus, were then aligned using a pairwise method. This pairwise alignment differed from the Clustal alignment in only two places, where a gap inserted in both sequences on the Clustal was removed in the pairwise alignment.
The pairwise method was then used to align the nucleic sequences of B.taurus and R.norvegicus. The pairwise nucleic alignment was translated back to amino acid sequence using Seaview and the result did not resemble the Clustal amino acid alignments or the pairwise amino acid alignments. This was unexpected. The downloaded nucleotide sequences were much longer than they should be if they were just the amino acid counterparts, which could possibly be responsible for the highly unaligned ends of the DNA pairwise alignment. Swami was also chopping off about 80 base pairs from the beginning of the DNA sequences for some sort of labeling reason. I would expect the pairwise nucleic alignment and amino acid pairwise alignment to greatly differ when synonymous substitution rates are high within the gene or if the two sequences compared are not in decent alignment.
The LALIGN function was used to find the best local alignments between the amino acid sequences from B.taurus and R.norvegicus. This alignment was very similar to the pairwise alignment generated previously of the amino acid sequences using ALIGN. These alignments would differ dramatically if the two sequences in question were dramatically different in size, as the global alignment would feature many more gaps in order to align every residue while the local alignment would place more care within aligning similar motifs, while the local alignment would focus more upon similar motifs.

ADH7 alcohol dehydrogenase 7. (2011, March 7). Retrieved from

Week 3


Sonja Harrower
BIO 335
Week three exercises

1) The analysis for the TERT should be done at the protein level, while TERC should be done at the nucleic acid level since it is never even translated. By analyzing TERT at the protein level, greater insight of the functional domains can be gained.
2) I increased the penalties for gap opening and extension for the alignment of the TERC because I wanted to avoid greatly extending the data just to make them align since there are sections known to differ among species.
The penalties for the protein alignment of TERT were initially set lower than those for nucleic acids, so I left them as they were.
3) The DNADIST command on Workbench 3.2 was used to compare the evolutionary distance of the nucleic acid sequences. The greater the number in the matrix the greater the difference between the two sequences compared.
Table 1: TERC comparison of evolutionary distance using DNADIST of nucleic acids. (1)M.mulatta (2)H.sapiens (3) O.cuniculus (4) S.scrofa (5)B.taurus (6) E.caballus (7)F.catus (8)R.norvegicus (9)M.musuculus (10)X.laevis (11)G.gallus
Table 2: TERT comparison of evolutionary distance using DNADIST of nucleic acids. (1)M.musculus (2)R.norvegicus (3)M.mulatta (4)H.sapiens (5)B.taurus (6)E.caballus (7)F.catus (8)S.scrofa (9)X.laevis (10)G.gallus (11)O.cuniculus

The averages of these numbers were calculated, 0.4556 and 0.7571 for the groups of TERC and TERT sequences respectively. Based on these averages, the TERT component of telomerase is evolving more quickly.
4) The functional domains will be more greatly conserved than other sections of the sequences. functional domain for the TERC component within the human reference sequence could begin around the 45 nucleic base where the sequences all start to fall into alignment. For the TERT sequence the functional domains seems to begin at the 104 nucleic acid residue in the human reference sequence, where there is a start codon.

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++Exercises….under files