BCHB-524 Bioinformatics Computing (Python)

Data for the course

Lecture topics and exercises:

0. BCHB-524 - Bioinformatics Computing Course Description
1. Introduction to Python - 1: Hello world, simple numbers
2. Introduction to Python - 2: Simple numbers, dna sequence
3. Introduction to Python - 3: Functions, if statement
4. Introduction to Python - 3: If and for statements
5. Introduction to Python - 3: DNA as a string
6. Introduction to Python - 3: Re-usable programs, handling input and output
7. Python Data Structures: Lists
8. Advanced Python Data Structures: Dictionaries, sets, files
9. Basic Python Review: Data structures
10. Advanced Python Idioms: Iteration, comprehensions, functional programming
11. Python Modules and Basic File Parsing: os, math, urllib, xml files
12. Sequence File Parsing using Biopython: Bio.SeqIO, Bio.SeqRecord
13. NGS Files and Pysam: Count reads, filter, SNPs
14. Protein Structure Informatics Using Biopython: Bio.PDB
15. XML Files and ElementTree: XML format, parse methods
16. Advanced Python Concepts: Modules
17. Advanced Python Concepts: Exceptions
18. Advanced Python Concepts: Object Oriented Programming
19. Advanced Python Concepts: OOP & Inheritance
20. Project Descriptions
21. Using Web-Services: NCBI E-Utilities, Online Blast
22. Using Local Tools: Blast
23. Relational Databases: SQL Basic Concepts
24. Relational Databases: Object Relational Mappers - SQLObject
25. Relational Databases: Object Relational Mappers - SQLObject II

Homework

• HW 1
  • 2.1 - Print Met codon backwards in lowercase
  • 2.2 - Find the position and translation frame of first start-codon in sequence
• HW 2
  • 3.1 - For anthrax gene: start codon in frame 1, nuc count, AA count, GC content
  • 4.1 - Compute reverse complement codon function
  • 4.2 - Check primer for tandem repeats
• HW 3
  • 6.1 - Compute reverse complement of a given NCBI Probe primer
  • 6.2 - Script that tests if reverse complement of primer is a palindrome
• HW 4
  • 8.1 - 3 ways to write a DNA reverse complement function
  • 8.2 - Script that takes a codon table and sequence and outputs the AA sequence
• HW 5
  • 9.1 - Modify DNA translation program (8.2) to translate in each forward and reverse frame, and handle "N" symbols in third position of a codon
  • 10.1 - Compact reverse complement function
  • 10.2 - Script that computes nucleotide frequency using a dictionary
• HW 6
  • 11.1 - Read "data.csv" and compute mean, stdev for values of specific gene by group and all together
  • 12.1 - Get AA frequency for all genes in RefSeq and UniProt human proteome files and compare the two
• HW 7
  • 15.1 - Write program to print references from a UniProt.xml file
  • 16.1 - MyDNAStuff module to translate AA sequence in all 6 reading frames
• HW 8
  • 17.1 - Add try/except blocks to DNA and codon_table modules from lec 16
  • 18.1 - Convert modules for DNA seq and codon tables to classes, use classes to translate an AA sequence
• HW 9
  • 21.1 - Blast query human gene and find mouse equivalents
  • 22.1 - Local Blast list of protein sequences against local database
• HW 10
  • 23.1 - SQL lookup scientific name of user-supplied organism
  • 24.1 - SQLObject lookup scientific name of user-supplied organism
• HW 11
  • 25.1 - Use SQLObject to find lineage of a user supplied organism name