Bioinformatics

Science programme: Genomic technologies

Our bioinformatics team has a wide range of skills: life molecular biology, biometrics, and information technology. We provide bioinformatics expertise to our clients through:

• Database development
• Custom data mining
• Oligonucleotide design for micro array experimentation.

Our team has designed and implemented biological and management databases. These databases service the annotation of mRNA & cDNA, metabolomic data, and the management of intellectual property.

Our BioPipe sequence analysis and annotation system has been used to annotate 550,000 sequences from HortResearch plant, insect, and fungal genome explorations projects as well as annotation of sequences derived from public domain sources (for example, Bombyx mori ).

The goal of BioPipe is to provide functional annotation by inference from searches against genes of known function. The BioPipe sequence annotation system incorporates motif detection, micro-satellite scanning, intron prediction, oligonucleotide primer design and selection, and sequence similarity searching tailored to individual genomes of interest, automated and semi-automated removal of contaminating sequence data (E. coli & vector) after sequence entry.

BioView incorporates tools to cross reference annotated sequences to proprietary patent information sources (GENESEQ™, Derwent Information Systems) where appropriately licensed. BioPipe has been developed to take advantage of pre-existing computation infrastructure that may not necessarily be available 24 x 7. It is currently deployed on Linux platforms but will operate under any form of UNIX.

BioPipe is made accessible via our web-based custom mining tool BioView. BioView is a comprehensive viewer system to BioPipe annotated sequence data that facilitates:

• Data mining of BioPipe databases
• Tracking and capture of mining efforts within a database
• Mining by individuals
• Mining by teams focused on the same goals
• Capture of researcher expertise and knowledge through manual annotations
• Additional sequences analysis (using EMBOSS and other tool kits).

We can provide organisations with sequence annotation using our BioPipe sequence analysis and annotation system, either for annotation of their own sequences, or by accessing pre-annotated sequences data from Malus, Actinidia, Vaccinium, or Bombyx mori.