New EST trimming procedure applied to SUCEST sequences
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
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Trimming procedures are an important part of the sequence analysis pipeline in an EST Sequencing Project. In general, trimming is done in several phases, each one detecting and removing some kind of undesirable artifact, such as low quality sequence, vectors or adapters, and contamination. However, this strategy often results in a phase being unable to recognize its target because part of it was removed during a previous phase. To remedy this drawback, we propose a new strategy, where each phase detects but does not remove its target, leaving this decision to a post processing step occurring after all phases. Our tests show that this strategy can significantly improve the detection of artifacts.