PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design

Author

Kushwaha, Garima ; Srivastava, Gyan Prakash ; Xu, Dong

Author_Institution

C.B. Life Sci. Center, Univ. of Missouri, Columbia, MO, USA

fYear

2011

fDate

12-15 Nov. 2011

Firstpage

345

Lastpage

351

Abstract

Highly specific and efficient primer/probe design in high-throughput manner has been in demand for genomic research. Here we present PRIMEGENSw3 (http://primegens.org), a set of web-based utilities for high-throughput primer/probe design. These utilities allow users to select genomic regions and to design primer/probe for selected regions in an automatic fashion. It runs the PRIMEGENSv2 algorithm in backend on a high-performance server and uses the locally stored genomic database or any user-provided dataset for cross-hybridization check. Cross- hybridization is assessed not only using BLAST but also by checking mismatch positions and energy calculation of potential hybridization hits. The results can be visualized online in a tabular format and also can be downloaded. In addition, the web server supports primer design for methylated sequences, which is used in epigenetic studies. Stand-alone version of the software is also available for download at the website.

Keywords

Internet; biology computing; data visualisation; genomics; molecular biophysics; PRIMEGENSw3 tool; Web-based tool; cross-hybridization check; epigenetics; genomic database; genomic region; genomic research; methylated sequence; primer design; probe design; tabular visualization; Algorithm design and analysis; Bioinformatics; Databases; Genomics; Probes; Servers; Thermodynamics; PCR primer; PRIMEGENS; bisulfite sequencing; crosshybridization; primer-design; probe;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on

Conference_Location

Atlanta, GA

Print_ISBN

978-1-4577-1799-4

Type

conf

DOI

10.1109/BIBM.2011.43

Filename

6120464