TY - JOUR
AU - Hwang, Pei-Ing
AB - Background: The enormous amount of sequence data available in the public domain database has been a gold mine for researchers exploring various themes in life sciences, and hence the quality of such data is of serious concern to researchers. Removal of vector contamination is one of the most significant operations to obtain accurate sequence data containing only a cDNA insert from the basecalls output by an automatic DNA sequencer. Popular bioinformatics programs to accomplish vector trimming include LUCY, cross_match and SeqClean. Results: In a recent study, where the program SeqClean was used to remove vector contamination from our test set of EST data compiled through various library construction systems, however, a significant number of errors remained after preliminary trimming. These errors were later almost completely corrected by simply using a re-linearized form of the cloning vector to compare against the target ESTs. The modified trimming procedure for SeqClean was also compared with the trimming efficiency of the other two popular programs, LUCY2, and cross_match. Using SeqClean with a re-linearized form of the cloning vector significantly surpassed the other two programs in all tested conditions, while the performance of the other two programs was not influenced by the modified procedure. 
TI - An optimized procedure greatly improves EST vector contamination removal
JF - BMC Genomics
DO - 10.1186/1471-2164-8-416
DA - 2007-11-13
UR - https://www.deepdyve.com/lp/springer-journals/an-optimized-procedure-greatly-improves-est-vector-contamination-CPiswbj2o2
SP - 1
EP - 11
VL - 8
IS - 1
DP - DeepDyve
ER -