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be used individually in each case. Another standard task is to run a web server that offers

e.g. a software like BLAST, which in turn can be used by other users for their analyses. To

do this, you can simply install the BLAST server yourself by downloading it from the

NCBI website: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_

TYPE=Download. However, it must be said that this requires some prior knowledge.

Examine/Analyze Data

Data can be analyzed particularly well with R, Perl and Python. In particular, Perl allows

you to formulate so-called “regular expressions”, which test whether a certain expression

occurs in a text, file, or database (e.g., with an A at the beginning or exactly two “t”s at the

end of a line). https://regexr.com explains in more detail how to describe these searches

correctly.

A tutorial for Perl is available here (https://perlmaven.com/perl-­tutorial), which covers

typical introductory topics for programming with Perl such as installation, debugging and

command line, and explains terms such as scalars (strings, operators), files and arrays.

Also useful is the book Perl in 21 days (by Patrick Ditchen; https://www.google.com/url?

sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjI2PbduI

HrAhUDx4sKHZmCCwUQFjACegQIARAB&url=http%3A%2F%2Fstarkill.synology.

me%2Fuwe%2FPerl21%2F26393_21t_perl.pdf&usg=AOvVaw0FnAy8RM8Pv3CWeM

HN2r0-­), which gives a step by step introduction to programming with Perl.

In addition, there are other programming languages such as C++ and Julia, but also

web-based programming environments such as Jupyter Notebook, which support various

languages such as Julia, Python and R. For this you are welcome to inform yourself on the

internet depending on your interest.

Understand (or Model) Data

We have explained this in detail in the book and tutorial. This can be done especially well

with the tools Cytoscape, CellDesigner and SQUAD or Jimena – and then more elabo­

rately with self-written programs.

This is already a brief overview of programming. But if you want to know more and

practice, you will now find an overview of programming languages and what they do,

including tutorials.

Programming Languages and Tutorials

Perl

Perl (Practical Extraction and Report Language): This programming language is very

popular in bioinformatics because it is very good for processing long lists and compiling

them into new lists.

19  Tutorial: An Overview of Important Databases and Programs