2020-02-19 13:18 by pjotrp

1 Bioinformatics

Quick links:

  1. GenFrag
  2. BioNode

The Laboratory of Nematology pursues computational biology as an integrated scientific discipline. Not only do we write our own software, we also contribute to important open source software projects, such as BioRuby1, BioScala, BioLib and R/qtl2.

We have facilities for running bioinformatics tools on a computing cluster, and in the Cloud.

1.1 Software

The following software was created and released in collaboration with our laboratory:

MQM for R/qtl

R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL) for the R statistical environment. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with other methods2.

See http://www.rqtl.org/

GenFrag

GenFrag predicts cDNA-AFLP transcript derived fragments. Upload a FASTA file and define a search for restriction enzymes and adapters.

See http://genfrag.biobeat.org/

GenEST

GenEST provides a bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP3.

BioNode

BioNode is a Debian VM for bioinformatics that runs on the desktop (on VirtualBox) and scales in the lab, and even the Cloud (on Amazon).

See http://biobeat.org/bionode

1.2 Information

For more information on software and publications see the website of Pjotr Prins


Bibliography

1. Goto, N. et al.BioRuby: bioinformatics software for the Ruby programming language, Bioinformatics, 26, 2617-2619 [2010]. [DOI]
2. Arends, D., Prins, P., Jansen, R. C. & Broman, K. W.R/qtl: high-throughput multiple QTL mapping, Bioinformatics, 26, 2990-2992 [2010]. [DOI]
3. Qin, L. et al.GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP, Nucleic Acids Res, 29, 1616-1622 [2001]. [Link]

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