Math 297/Biol 497
Biomolecular Computing in Nature
Projects: Graff. A Java tool for analysing ciliate DNA data.
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Abstract:
Throughout the semester, we have been using the NCBI website
to gather information about different ciliate species for many different
reasons. Mostly to analyze micronuclear DNA sequences for specific protein
strands. We can then manipulate the protein DNA sequences in order to model
theories in the world of bio-molecular computing that try to model how the cell
creates macronuclear DNA from it's micronuclear DNA.
I am writing a
program using Java that will make extracting information from NCBI much simpler and allow
individuals to focus on the application of the information. The program
will:
-Count the number of each nucleotide that appears in the sequence
(i.e. A's, C's, T's, and G's)
-Count the number of pairs of each possible
pair of nucleotides(i.e. AA's, AC's, AT's, AG's,.....GT's, GG's)
-Extract IES
sequence locations if referenced on NCBI webpage
-Extract MDS
sequence locations if referenced on the NCBI webpage
-Ability to
search any sequence, IES, or MDS for a specific pattern input from the
user
-Suggested implementation: Ability to search for hypothesized chromosome
fragmentation locations