I wrote DOGMA as a Molecular Biology tool which I could use for my Lab Methods course, and for future use in doing whatever research I do.
DOGMA is an interesting application, based entirely on PHP functions. DOGMA employs the use of regular expressions which are, when worded properly, rediculously efficient when it comes to the analysis of the different elements in molecular biology.
DOGMA stands for Discrete Operations for Genetic Manipulation and Analysis. For the most part, there are a series of functions whereby the output of one function becomes the input of the next. The order is fairly well structured in that it mimics what is observed in biological systems.
The following functions are available in DOGMA:
- DNA, RNA, Amino Acid Sequence Input
- Reformatting of sequence by reading frame.
- Complimentary Strand Synthesis
- Transcription
- Translation
- Of any 6 open reading frames
- Advanced searching
- User written Regular Expressions
- Palindromic sequences
- Ability to search for vague sequences
- Search of complimentary strand
- Restriction Enzymes
- Use of REBASE Restriction Enzyme data
- Identification of Restriction Enzymes based on search parameters
- Cross-referencing
- Infinite restriction digests
