Email updates

Keep up to date with the latest news and content from BMC Systems Biology and BioMed Central.

This article is part of the supplement: Proceedings of the 23rd International Conference on Genome Informatics (GIW 2012)

Open Access Open Badges Proceedings

Palindromic sequence impedes sequencing-by-ligation mechanism

Yu-Feng Huang1, Sheng-Chung Chen1, Yih-Shien Chiang2, Tzu-Han Chen1 and Kuo-Ping Chiu123*

Author Affiliations

1 Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei 115, Taiwan

2 NGS core, TechCom division, National Taiwan University, Taiwan

3 Institute of Zoology, National Taiwan University, Taiwan

For all author emails, please log on.

BMC Systems Biology 2012, 6(Suppl 2):S10  doi:10.1186/1752-0509-6-S2-S10

Published: 12 December 2012



Current next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Although the pros and cons for each sequencing mechanism have more or less been discussed in a number of occasions, the potential obstacle imposed by palindromic sequences has not yet been addressed.


To test the effect of the palindromic region on sequencing efficacy, we clonally amplified a paired-end ditag sequence composed of a 24-bp palindromic sequence flanked by a pair of tags from the E. coli genome. We used the near homogeneous fragments produced from MmeI digestion of the amplified clone to generate a sequencing library for SOLiD 5500xl sequencer.


Results showed that, traditional ABI sequencers, which adopt sequencing-by-synthesis mechanism, were able to read through the palindromic region. However, SOLiD 5500xl was unable to do so. Instead, the palindromic region was read as miscellaneous random sequences. Moreover, readable tag sequence turned obscure ~2 bp prior to the palindromic region.


Taken together, we demonstrate that SOLiD machines, which employ sequencing-by-ligation mechanism, are unable to read through the palindromic region. On the other hand, sequencing-by-synthesis sequencers had no difficulty in doing so.