7

for the search. In this way, you can match domain by domain in the protein with a new

BLAST search each time for the sequence portion that has not yet been matched by the

search. Finally, in difficult cases, the BLAST search may only reveal a similarity to a data­

base entry that has no clear function. In this case (protein sequence), you can use the

“position-specific iterative BLAST”, or Psi-BLAST for short, which then searches with all

the still unrecognized sequences at the same time (a so-called “profile”) until it lands a hit

to which a sequence can be assigned. This almost always works, but may take several

repetitions. You should also only continue searching with Psi-BLAST if something

changes in the repeat search, otherwise the search is “converged” in vain.

1.2

https://www.rcsb.org/pdb/home/home.do

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1.1

How Do I Start My Bioinformatics Analysis? Useful Links

and Tools

Generally speaking, we first look at the function of the molecule we want to bioinformati­

cally determine by comparing it directly to a database. The best known example is the

direct sequence comparison with BLAST, which we have already discussed in detail. The

next step is to use other databases or programs for analyses and comparisons to obtain

additional information. A simple example is to search for secondary data, and our first

example of this was the protein database. As a primary database, it contains the three-­

dimensional coordinates of protein structures, but it also contains a lot of secondary data

about these proteins where this structure determination was successful. As a third step, we

can finally follow up with detailed analyses.

In the following, useful supporting sites for these steps are briefly presented. The

BioNumbers database describes number relationships in biology (https://bionumbers.hms.

harvard.edu). This was established at Harvard University by students who first calculated

these biological problems and then made these numbers available to the interested reader.

Unfortunately, most bioinformatics websites are in English, including this book. This is

due to the fact that the Anglo-Americans were simply faster with many initial develop­

ments than German bioinformatics. In addition, English is now the language of science,

and the creator of a bioinformatics website would like everyone to be able to use this site.

1.1  How Do I Start My Bioinformatics Analysis? Useful Links and Tools