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This is a description of objects used in DNA/Genomics software development. I need to ﬁrst come up with such a list, and the relationship between them to base any further software development of a sw library.
Each object is described and listing of what other objects it contains and what attributes the objects has.
Each object will be represented as a class. The object attributes will help to deﬁne the access methods of the object.
contains: contig objects. one DNA Molecule
contains: physical position object, cytogenetic position object.
physical position of contig in the chromosom.
Attributes (these are estimates from RH map positions):
Cytogenetic position of contig in the chromosom.
Attributes (based on annotation from GenBank entry)
DNA molecule (or DNA sequence)
contains number of Gene objects, contains one sequence of DNA base pairs objects.
contains number of exons and number of introns.
exon. a region in a gene that is a coding region for protein. Contains number of codons, and a DNA sequence.
intron. a region in a gene that is a not a coding region for protein. Contains a DNA sequence