[ 675COSCAPR18 ] Module Applied Programming

Workload Mode of examination Education level Study areas Responsible person Coordinating university
3 ECTS Accumulative module examination B1 - Bachelor's programme 1. year Computer Science Vohnoutov√° Marta USB Budweis
Detailed information
Original study plan Bachelor's programme Bioinformatics 2018W
Objectives Knowledge of Applied Programming
Subject Biopython The ability to parse bioinformatics files into Python utilizable data structures, including support for the following formats:

  • Blast output both from standalone and WWW Blast
  • Clustalw
  • GenBank
  • PubMed and Medline
  • ExPASy files, like Enzyme and Prosite
  • SCOP, including 'dom' and 'lin' files
  • UniGene
  • SwissProt

Files in the supported formats can be iterated over record by record or indexed and accessed via a Dictionary interface. Code to deal with popular on-line bioinformatics destinations such as:

  • NCBI Blast, Entrez and PubMed services
  • ExPASy Swiss-Prot and Prosite entries, as well as Prosite searches Interfaces to common bioinformatics

programs such as:

  • Standalone Blast from NCBI
  • Clustalw alignment program
  • EMBOSS command line tools

A standard sequence class that deals with sequences, ids on sequences, and sequence features. Tools for performing common operations on sequences, such as translation, transcription and weight calculations. Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines. Code for dealing with alignments, including a standard way to create and deal with substitution matrices. Code making it easy to split up parallelizable tasks into separate processes. GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc. Extensive documentation and help with using the modules, including this file, on-line wiki documentation, the web site, and the mailing list. Integration with BioSQL, a sequence database schema also supported by the BioPerl and BioJava projects.

Corresponding lecture 675COSCWOS1: Working with Operating Systems (3 ECTS)
Subordinated subjects, modules and lectures