Per Unneberg

SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra

This article presents SOMCD, an improved method for the evaluation of protein secondary structure from circular dichroism spectra, based on Kohonens self‐organizing maps (SOM). Protein circular dichroism (CD) spectra are used to train a SOM, which arranges the spectra on a two‐dimensional map. Location in the map reflects the secondary structure composition of a protein. With SOMCD, the prediction of β‐turn has been included. The number of spectra in the training set has been increased, and it now includes 39 protein spectra and 6 reference spectra. Finally, SOM parameters have been chosen to minimize distortion and make the network produce clusters with known properties. Estimation results show improvements compared with the previous version, K2D, which, in addition, estimated only three secondary structure components; the accuracy of the method is more uniform over the different secondary structures. Proteins 2001;42:460–470.

Analysis of 70,000 EST sequences to study divergence between two closely related Populus species

The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.

Shotgun sequencing and microarray analysis of RDA transcripts

Monitoring of differential gene expression is an important step towards understanding of gene function. We describe a comparison of the representational difference analysis (RDA) subtraction process with corresponding microarray analysis. The subtraction steps are followed in a quantitative manner using a shotgun cloning and sequencing procedure that includes over 1900 gene sequences. In parallel, the enriched transcripts are spotted onto microarrays facilitating large scale hybridization analysis of the representations and the difference products. We show by the shotgun procedure that there is a high diversity of gene fragments represented in the iterative RDA products (92-67% singletons) with a low number of shared sequences (<9%) between subsequent subtraction cycles. A non redundant set of 1141 RDA clones were immobilized on glass slides and the majority of these clones (97%) gave repeated good fluorescent signals in a subsequent hybridization of the labelled and amplified original cDNA. We observed only a low number of false positives (<2%) and a more than twofold differential expression for 32% (363) of the immobilized RDA clones. In conclusion, we show that by random sequencing of the difference products we obtained an accurate transcript profile of the individual steps and that large-scale confirmation of the obtained transcripts can be achieved by microarray analysis.