Overview
Bioinformatics Software
 Category | Programs | Installation | Documentation | Updates |
|---|---|---|---|---|
| Sequence analysis | all common tools for
| * /afs/rzg/bioinfo/biosoft/ (Linux,IBM-AIX,SUN-Solaris) | /afs/rzg/bioinfo/biosoft/<tool name>/... | regular updates |
| MIGenAS toolkit: integrated sequence analysis (web application + SOAP web sevices) | http://www.migenas.mpg.de http://www.migenas.org | online, published in NAR | actively developed, regular updates | |
| Genome annotation | GenDB 2.2: a tool for automatic and manual annotation of prokaryotic genomes | https://www.bioinfo.mpg.de/gendb22 (GenDB 2.2) | published in NAR | bugfixes |
| HaloLex: comprehensive annotation and information system for prokaryotic genome and proteome data | http://www.halolex.mpg.de | online | actively developed by MPI of Biochemistry and RZG | |
| Genome Assembly | consed, parallel portable Linux version of phrap and crossmatch, | on request | on request | - |
| Visualization | Tree viewers, alignment editors, structure viewers | /afs/rzg/bioinfo/soft/visualization/ | /afs/rzg/bioinfo/soft/visualization/... | regular updates |
* /afs/rzg is a shortcut (CellAlias) for /afs/ipp-garching.mpg.de. It is equivalent to /afs/ipp or /afs/ipp-garching.mpg.de/
Databases
| Type | Databases | Formats | Indexes | Location | Updates |
|---|---|---|---|---|---|
| public sequence databases | UniProt(swissprot,TrEMBL),nr,nt,pdb,... | fasta | NCBI blast | /bio/db/, /afs/rzg/bioinfo/pub_db/ | weekly (Sat) |
| UniProtKB(swissprot,TrEMBL) | XML | - | /bio/db/XML/uniprot/ | biweekly (Sat) | |
| iProClass | XML | - | /bio/db/XML/iProClass/ | biweekly (Sat) | |
| completed public genomes | >550 prokaryotic strains, ~10 eukaryotic | fasta,gbk | NCBI blast | /bio/db/, /afs/rzg/bioinfo/pub_db/ | weekly (Sat) |
| Protein structures | PDB | pdb (atom coordinates) | - | /bio/db/PDB/ | weekly (Sat) |
Dedicated Compute Resources
Besides general resources which are open to all RZG users there are dedicated compute and storage facilities for computational biology projects.
| IBM Blade Center linux cluster (blade center oe, 28 dual-core Intel 64-bit Woodcrest CPUs) | MPI of Biochemistry, MIGenAS |
| SUN FIRE linux cluster (eva cluster 128 dual-core AMD 64-bit Opteron CPUs) | MPI of Evolutionary Anthropology |
