Genetic Construct is a program that generates a visual construct of a genetic sequence. I programmed it in Python programming language for the visual exploration of genetic sequence constructs to discover genetic patterns that could be the genetic signature for gene regulatory switches, or protein motifs and structural domains, biologically important in gene control and protein function.
I have included two DNA sequences with the program, the complete sequence of the Human FMR1 gene (NG_007529.fa) obtained from NCBI Nucleotide Database and the coding sequence of Human TRO gene (CCDS_43959.fa) from the CCDS database. The following are construct images generated from these sequences:
Construct FMR1
Construct FMR1 CGG
Construct TRO
The FMR1 gene has a CGG trinucleotide repeat that is known to be mutated by expansion in fragile X syndrome. The construct of the 46kb sequence of the FMR1 gene clearly reveals a visual band of the CpG island adjacent the CGG trinucleotide repeat, and the construct with the CGG pattern displayed further highlights the CGG repeat. In examination of the constructs of several coding sequences from the CCDS database, I discovered that the construct of the 4kb coding sequence of the TRO gene has strong repetitive feature that denotes a previously known repeat region believed to be a prominent structural feature of the encoded trophinin protein.
In future releases of the Genetic Construct program I plan to add new capabilities to further the usefulness of the construct in genetic exploration.
Submitted by Jim on October 7, 2010 at 7:00 pm
