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BioMed Research International
Volume 2013 (2013), Article ID 905429, 9 pages
http://dx.doi.org/10.1155/2013/905429
Research Article

SeedSeq: Off-Target Transcriptome Database

1Indian Association for the Cultivation of Science, Kolkata, West Bengal 700032, India
2Gyanxet, BF 286 Salt Lake, Kolkata, West Bengal 700064, India
3Medical Faculty, Technical University of Dresden, 1307 Dresden, Germany
4Universitätsklinikum Dresden, Blasewitzer Straße 43, 01307 Dresden, Germany

Received 21 April 2013; Revised 27 June 2013; Accepted 1 July 2013

Academic Editor: Yudong Cai

Copyright © 2013 Shaoli Das et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs). However, owing to a tolerance for mismatches and gaps in base-pairing with target transcripts, siRNAs could have up to hundreds of potential target sequences in a genome, and some small RNAs in mammalian systems have been shown to affect the levels of many messenger RNAs (off-targets) besides their intended target transcripts (on-targets). The reference sequence (RefSeq) collection aims to provide a comprehensive, integrated, nonredundant, well-annotated set of sequences, including mRNA transcripts. We performed a detailed off-target analysis of three most commonly used kinome siRNA libraries based on the latest RefSeq version. To simplify the access to off-target transcripts, we created a SeedSeq database, a new unique format to store off-target information.