After we have become acquainted with the sequence analysis of proteins, RNA molecules

and DNA as basic techniques of bioinformatics and have already looked at their interac­

tion in the form of metabolic and regulatory networks (Part I), we will now provide an

in-depth insight into basic strategies of bioinformatic working methods in Part II.

From a Computer-Technical (Informatics) Point of View, Three Points

Are Interesting

1. In order to cope with the large amounts of data, good databases are important, in which

one can search particularly efficiently and accurately (e.g., database indexing).

Likewise, because of the abundance of data, search capabilities that are as fast as pos­

sible are crucial to shorten exact, lengthy computations as efficiently as possible (heu­

ristic searches, Chap. 6, e.g., BLAST).

2. Actually, bioinformatics is always about cracking codes to understand biological pro­

cesses. How does one measure (according to Shannon) the amount of information hid­

den in biological messages? And how do you crack the codes as efficiently as possible

(Chap. 7, e.g. with sequence analyses)?

3. How long do computers actually need for a calculation? Problems become especially

difficult with built-in combinatorics. In this case, the computer needs a multiple of

computing time for just one unit more (NP problems). We get to know typical problems

of this kind from bioinformatics, how they are solved and when only a larger computer

helps (Chap. 8).

Part II

How Do I Understand Bioinformatics?