Authors: allegra.via Via or St├®phane Plaisance
This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.
Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...
Keywords: Pattern matching, Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file.
Scientific topics: Bioinformatics
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.
Keywords: Programming, Python, Python biologists
This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused.
The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites.
Here you can find:
A definition of linear motifs and...
Keywords: Bioinformatics
This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list data structure. The...
Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing
Introductory lecture to the Unix/Linux command-line
Description of the computer shell and the command-line interface
Differences between graphical and command-line interfaces
The most commond Unix/Linux commands are provided
Keywords: Bioinformatics, Programming, Unixlinux