84

Useful Tools and Web Links

BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi

NCBI

https://www.ncbi.nlm.nih.gov/pubmed/

EBI

https://www.ebi.ac.uk/services

SBI

https://www.sib.swiss/

UniProt

https://www.uniprot.org/

PDB

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

STRING

https://string-­db.org/

YANAsquare

https://www.bioinfo.biozentrum.uni-­wuerzburg.de/

computing/yanasquare/

BioPerl

https://bioperl.org/

Biojava

https://biojava.org/

Numerical recipies

https://numerical.recipes/

Literature

Christiansen T, Torkington N (2003) Perl cookbook. Solutions & examples for Perl programmers.

O’Reilly Media, Beijing (Final Release Date: August 2003, Pages: 968 *This book is simply very

well written and provides a very good introduction to the Perl programming language)

Hansen A (2013) Bioinformatik: Ein Leitfaden für Naturwissenschaftler. Birkhaeuser, Basel.

(Erstveröffentlichung 2004, isbn 3-7643-6253-7, Taschenbuchauflage – 4. Oktober 2013)

Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007) Numerical recipes, 3rd edn. The art

of scientific computing (English) Bound edition. Cambridge University Press, New York. isbn

978-0-521-88068-8

Here are some more book suggestions for Perl and its programming that are not explicitly discussed

in the chapter. For other programming languages please look in the tutorial (later chapter in

the book)

Angly FE, Fields CJ, Tyson GW (2014) The bio-community Perl toolkit for microbial ecology.

Bioinformatics 30(13):1926–1927. https://doi.org/10.1093/bioinformatics/btu130

Mount D (2004) Bioinformatics: sequence and genome analysis, 2. Aufl. Cold Spring Harbor

Laboratory Press, Cold Spring Harbor, New York (© 2004 • 665pp., illus., appendices, index

paperback, isbn 978-087969712-9 *David Mount also does a very good job of introducing the

underlying algorithms of sequence analysis. However, it is aimed at somewhat advanced stu­

dents. Also used as a textbook at LMU Munich)

Stajich JE, Block D, Boulez K et al (2002) The bioperl toolkit: Perl modules for the life sciences.

Genome Res 12(10):1611–1618

Tisdall J (2001) Beginning Perl for bioinformatics an introduction to Perl for biologists. 1. Aufl.

O’Reilly Media, Sebastopol, Kalifornien, USA (Final Release Date: October 2001, Pages 386)

Vos RA, Caravas J, Hartmann K et al (2011) BIO: phylo-phyloinformatic analysis using Perl. BMC

Bioinformatics 12:63. https://doi.org/10.1186/1471-­2105-­12-­63

6  Extremely Fast Sequence Comparisons Identify All the Molecules That Are Present…