Title

Authors

Affiliation

VALWAY Technology Center, NEC Soft, Ltd., 1-18-7, Shinkiba Koto-ku, Tokyo 136-8627, Japan

Email

waga-iwao@mxc.nes.nec.co.jp; *Corresponding author

Article Type

Software

Date

Received May 12, 2011; Accepted June 21, 2011; Published August 20, 2011

DNA or RNA aptamers have gained attention as the next generation antibody-like molecules for medical or diagnostic use. Conventional secondary structure prediction tools for nucleic acids play an important role to truncate or minimize sequence, or introduce limited chemical modifications without compromising or changing its binding affinity to targets in the design of improved aptamers selected by Systematic Evolution of Ligands by EXponential enrichment (SELEX). We describe a novel software package, ValFold, capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm.

Keywords

aptamer, SELEX, aptamer truncation, secondary structure prediction

Availability

http://code.google.com/p/valfold/

Citation

Akitomi et al. Bioinformation 7(1): 38-40 (2011)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.