We provide support/services for sequence assembly, mapping (e.g., Illumina on 454 transcriptomes), contig annotation, cluster-analysis, phylogenenetic placement, metagenome / -transcriptome functional comparative analysis, ...

arb is a software environment primarily for ribosomal DNA sequence data, used by several working groups at the AWI. The bioinformatics group provides a platform and user support concerning arb.

Some arb links:

• The arb project
• The Microbial Genomics Group at the MPI Bremen
• The SILVA database

Course material (7.3.2007):

• Power Point slides
• pdf version of the arb manual (from download.arb-home.de/documentation/arb.ps)
  
  
  

The Staden package is a modular sequence analysis system, originally aimed at assembling genomic contigs. Due to its flexibility, it is used for several other tasks as well. Below is the material from our Staden introduction 2006.

• Staden course 2006
  
  
  

R is a flexible and powerful open source statistical analysis environment.

Links:

• R project
• CRAN
• SimpleR (a nice introductory script by R. Verzani)

POLMAR R-Course "Programming" (3/2017 Bremerhaven)
DAY 1

DAY 2

step4.R for multiple-file analyses, see prepmf.R (Day2-ZIP)

 R for Paleo modellers

ZIP ; NetCDFs found on csys-FS or biseqa:/tmp/R-Paleo/

Paleo-src.ZIP

Day1-ZIP incl. PPT-PDF

 Day2-ZIP incl data

Material for lecture on "Linear algebra in the exploration of climate processes" 

(in german)

eof-1.R

Motivation analyses (Rahmstorf 2003 d18O-data  and El Nino EOF1): sst_d18O.R

Material on Clustering, Mapping, CCA:

• CLUST.R
  
• LDA: training data, test data, Script
  
  

Contact

Prof.Dr. Stephan Frickenhaus
Dr. Lars Harms
Dipl. Bioinf. Stefan Neuhaus

former members:

      Dr. Fabian Kilpert [DFG]

Dr. Bánk Beszteri