Biomedical subjects

Anason S Halees

Publications and source records attributed to Anason S Halees.

4 recordsLinked to original sources

PubMed2004

PromoSer: improvements to the algorithm, visualization and accessibility.

PromoSer is a web service that provides an easy and efficient approach to the batch retrieval of a large number of proximal promoters. Since its introduction last year, it has undergone continued development and expansion. At the core, there have been improvements in the filtering of the raw mRNA/EST sequences upon which all predictions are built, improvements in the alignments clustering and transcription start site prediction algorithms, and improvements in the backing database for increased performance. At the user interface level, improvements include enhanced functionality and user options, better integration with other resources on the web and a new visualization tool. PromoSer now also supports queries using a SOAP-based interface and XML-based responses. The service is publicly available at http://biowulf.bu.edu/zlab/PromoSer.

Algorithms↗

PubMed2004

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

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. 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. We have adopted the client-side integration technology and built a consistent input and output environment with a versatile visualization tool named SeqVISTA. The infrastructure will allow for easy integration of gene regulation analysis software that is scattered over the Internet. It will also enable 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. SeqVISTA is freely available to academic users and can be launched online at http://zlab.bu.edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu.edu/SeqVISTA.

Algorithms↗

PubMed2004

Site2genome: locating short DNA sequences in whole genomes.

SUMMARY: Many biological papers describe short, functional DNA sites without specifying their exact positions in the genome. We have developed a Web server that automates the tedious task of locating such sites in eukaryotic genomes, thus giving access to the context of rich annotations that are increasingly available for genome sequences. AVAILABILITY: http://zlab.bu.edu/site2genome/

Algorithms↗

PubMed2003

PromoSer: A large-scale mammalian promoter and transcription start site identification service.

Proximal promoters have a major impact on transcriptional regulation. Studies of the sequence-based nature of this regulation usually require collection of proximal promoter sequences for large sets of co-regulated genes. We report a newly implemented web service that facilitates extraction of user specified regions around the transcription start site of all annotated human, mouse or rat genes. The transcription start sites have been identified computationally by considering alignments of a large number of partial and full-length mRNA sequences to genomic DNA, with provision for alternative promoters. The service is publicly available at http://biowulf.bu.edu/zlab/PromoSer/.

Animals↗