Making the most of phylogeny - OPUS - Universität Würzburg

Chapter 1.
Material
1.1. Hardware requirements
The main part of the calculations were carried out on a computer with SuSE 10.3
or SuSE 11.0 and sparse Microsoft Windows XP TM
as operating system, Intel R○
Core TM
2 6600 central processing unit (CPU) with 2.40 GHz and 2 GB DDR2-SDRAM
memory. Furthermore, I had access to a high performance computing (HPC) cluster
system and used it for longer calculations. The HPC cluster consists of 40 nodes
each having two dual core Intel R○ Xeon R○ 5140 (2.33 GHz) CPUs. Each node offers
8–16 GB of memory and a local 20 GB hard drive. The entire cluster additionally
holds 777 GB of network attached storage (NAS). This gives a total of 160 CPU cores,
448 GB memory and more then 1.5 TB storage.
1.2. Databases
These included the major public databases, starting from primary sequence information:
Genbank (Benson et al. 2000; Benson et al. 2009) at the NCBI, the EMBL
nucleotide sequence database at the European Molecular Biology Laboratory (EMBL)
(Baker et al. 2000; Leinonen et al. 2010), DNA Data Bank of Japan (DDBJ) (Kaminuma
et al. 2010; Tateno et al. 2000) and Universal Protein Resource (UniProt) (Jain et al.
2009; UniProt Consortium 2010). Furthermore, specific secondary databases such as
Simple Modular Architecture Research Tool (SMART) (Letunic et al. 2009; Schultz
et al. 1998) or Protein Families (PFAM) (Finn et al. 2010) were used.
Additionally we host some local installed databases using Postgres or MySQL
as database management system (DBMS) (e.g. tardigrade workbench (Förster et al.
2009), the BLAST2GO database (Götz et al. 2008) or the ITS2 database (Koetschan
et al. 2010)).
13