Integrated Platform for Regulatory Motif Detection: Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques have motivated the development of a large number of bioinformatics methods for the detection of regulatory motifs. Unfortunately, the regulatory process is extremely complex and individual computational algorithms typically have very limited success in genome-scale studies. Here we argue the importance of integrating multiple computational algorithms, and present an infrastructure that integrates eight web services covering key areas of transcriptional regulation. With innovated architecture and extended new functionalities, especially the pipeline management , the new infrastructure allows easy integration of gene regulation analysis software that is scattered over the Internet. It also enables bench biologists to perform an arsenal of analysis using cutting-edge methods in a familiar environment and bioinformatics researchers to focus on developing new algorithms without the need to invest substantial effort on complex pre- or post-processors.
Visual Data Mining: SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet. Our viewer may be launched on a GenBank record by a single click of a button installed in the web browser. SeqVISTA allows insights to be gained by viewing the totality of sequence annotations and predictions, which may be more revealing than the sum of their parts. SeqVISTA should run on any operating system with a Java 1.4 virtual machine, and it is freely available to academic users.
Please cite: SeqVISTA: A Graphical Tool for Sequence Feature Visualization and Comparison
|Zhenjun Hu , Bioinformatics Program, Boston University|
|Martin Frith , Bioinformatics Program, Boston University|
|Tianhua Niu , Program for Population Genetics, Harvard University|
|Zhiping Weng , Department of Biomedical Engineering, Boston University|