Calabria-Digital-Bio
Repository for my notes and computer programs written for my bioinformatics (digital biology) class.
My teammates for the class project are: Ms. Diana Medina and Ms. Selene Howe.
Our project repository is located at: /usr/local/share/digitalbiology/dbg0006. It is currently defunct.
Acknowledgements
Classmates
Teammates
I acknowledge that I have collaborated with my project teammates Ms. Diana N. Medina and Ms. Selene Y. Howe to complete this homework. Specifically, we discussed some hypotheses for homework assigned for Thursday, June 26, 2014, and how to test those hypotheses.
For Homework 2, we discussed different reasons for the variation between the different DNA sequences of GenomeA1, GenomeA2, and GenomeA3.
Other classmates
I also want to thank Ms. Priyadharshini Venkat, my classmate for this course, for giving me feedback about my hypotheses and helping me to find alternate golden models for the {\it Neurospora crassa} species.
Furthermore, I want to thank Ms. Priyadharshini Venkat and Ms. Elyssa Garza for explaining Phred quality scores in the context of the FastQ format for the {\it Neurospora crassa} species.
Besides, Ms. Oneida Ibarra helped me to understand the flow of genome assembly with BLAST+ and script for converting BLAST+ output file formats to GFF3 file format.
Class Instructor and Teaching Assistant
I also acknowledge the help that I have received from the course instructor, Prof. Rodolfo Aramayo, in getting back to my queries about the source of the reference sequence for the Neurospora crassa species that was provided to us on Tuesday. Prof. Aramayo also explained why the Perl scripts were for: converting BLAST+ output files in BLAST+ formats to GFF3 file format.
My teaching assistant, Mr. Ricardo Perez, has also helped me with different computing problems, and misunderstandings of genetics/genomics.
Others
In addition, I want to thank Ms. Tess L. Pham from the Tutor Zone at Evans Library, which is run by the Academic Success Center at Texas A&M University. Ms. Pham has tutored me about the basics of genetics and gave me feedback about the hypotheses which I proposed.
To be updated... To be updated... Fix this!!!
To be fixed... Must fix this!!! Will fix it.