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On the Pursuit of Optimal Sequence Trimming Parameters for EST Projects

Fabiano Cruz PeixotoJosé Miguel Ortega

In EST projects it is extremely important to be able to identify the informative region of the read, by trimming the non informative ones. Several methods for sequence trimming are available. In this work we present a methodology to compare such methods, based on the sequencing of defined sequences (pUC18 cloning vector) and homology searches to find the informative region using BLAST. This methodology has shown that Phred trim alt algorithm provides proper sequence trimming.

http://www.lbd.dcc.ufmg.br:8080/colecoes/wob/2002/007.pdf

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