This repo contains assignments from the BME160 course at UCSC which focused on programming in Python to manipulate biological data. I took this course in Spring 2021.
- converter.py: Convert from amino acid abbreviations to DNA/RNA codons and vice versa.
- coordinateMathSoln.py: Calculate bond length and angles between C-Ca-N.
- fastqParse.py: Filter out run data from FASTQ files.
- seqCleaner.py: Returns sequence with uppercase and replaces block of ambiguous bases with their count.
- proteinparams.py: Calculates protein properties such as molecular weight, amino acid composition, theoretical PI, etc.
- FastAreader.py: Reads FastA files for analysis.
- genomeAnalyzer.py: Calls FastAreader and nucparams and formats their outputs.
- nucparams.py: Calculates sequence properties such as amino acid composition and codon usage.
- sequenceAnalysis.py: Contains NucParams,FastAreader, and ProteinParams classes.
- findORFs.py: findORFs will be able to return possible ORFS for a set of parameters, including several start codon(s), stop codon(s), if longest gene is desired, and minimum gene length. Calls fastAreader and ORFfinder from sequenceAnalysis.py.
- sequenceAnalysis.py: Updated to include ORFfinder class to find all possible open reading frames.
- findUnique.py: Takes FASTA sequences of mitochondrial tRNA and returns unique (does not occur in any other sequence) and essential (minimized) tRNA sets.
- sequenceAnalysis.py: Inludes ORFfinder, NucParams, FastAreader, and ProteinParams classes.