Christian Baudet, Zanoni Dias
Published: March 31, 2006
Genet. Mol. Res. 5 (1) : 169-181

Cite this Article:
C. Baudet, Z. Dias (2006). Analysis of slipped sequences in EST projects. Genet. Mol. Res. 5(1): 169-181.

About the Authors
Christian Baudet, Zanoni Dias

Corresponding author
Z. Dias
E-mail: zanoni@ic.unicamp.br/zanoni@scylla.com.br

ABSTRACT

Slippage is an important sequencing problem that can occur in EST projects. However, very few studies have addressed this. We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291,689 EST sequences produced in the SUCEST project, we performed comparative tests between our proposed methods and the SUCEST method. The subsequence strategy is better than the suffix strategy, because it is not anchored at the end of the sequence, so it is more flexible to find slippage at the beginning of the EST. In a comparison with the SUCEST method, the advantage of our methods is that they do not discard the majority of the sequences marked as slippage, but instead only remove the slipped artifact from the sequence. Based on our tests the echo coverage method with subsequence strategy shows the best compromise between slippage detection and ease of calibration.

Key words: Expressed sequence tag, Sugar cane, Slippage, Sequence trimming.