DNA sequence

The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective) it is therefore important to have up-to-date knowledge about the various resources providing primary data.

For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection which is time consuming and requires considerable experience.

STREAM is the first publicly available framework for modeling, visualizing, and predicting the quantivative regulation of the transcription rate of a target gene.

Understanding transcriptional regulation of a gene in detail is a crucial step towards uncovering and ultimately utilizing the regulatory grammar of the genome. Modeling transcriptional regulation using thermodynamic equations has become an increasingly important approach towards this goal.

MPsrch is a biological sequence sequence comparison tool that implements the true Smith and Waterman algorithm. It allows an rigorous search in a reasonable computational time. MPsrch utilises an exhaustive algorithm, which is recognised as the most sensitive sequence comparison method available, whereas BLAST and FASTA utilise a heuristic one. As a consequence, MPsrch is capable of identifying hits in cases where BLAST and FASTA fail and also reports fewer false-positive hits.

This service provides an external access to the GeneWiz software developed at CBS (Pedersen AG et al. 2000)
The program visualizes DNA parameters and annotations in either a circular or linear representation.