The trimming performance of the three programs against CVS or RVS vectors were all compared in terms of number of incompletely-trimmed ESTs, number of low quality (e.g. shorter than 100 bases) ESTs discarded by a trimming program, and the average lengths of trimmed ESTs.
a number of ESTs whose length is equal to or greater than 100 bases after being processed by a vector trimming program as indicated Among all the tested conditions (three programs and two vector forms), SeqClean trimming against RVS markedly outperformed all the other conditions, delivering the lowest error rate without removing any additional ESTs (Table 3 and Additional file 1 for details).
Error rate of EST in this study indicates the ratio of ESTs which contained residual vector sequences (>12 base pairs) even after processing by a vector trimming program to the number of all the EST sequences subjected to the same trimming process.
Based on the observations above, a hypothesis was made that the trimming program neglected the circular form of the vector DNA which resulted in erroneous trimming of some of the EST sequences.
Prior to assembly, the reads were re-trimmed by the Figaro vector trimming program [10].
On the other hand, if vector does get overlooked by the trimming program, the short sequences will remain untrimmed.
Faced with the fragmentation of audiences and a decline in advertising revenue, broadcasters are trimming programming budgets, and unscripted shows are generally less expensive than fictional dramas, movies or other fare.
To further investigate whether our modified procedure is generally applicable to most cloning vectors with SeqClean processing, and how this procedure could affect the performance of other software, two other popular trimming programs, cross_match and LUCY2, and an additional three sets of ESTs downloaded from Trace Archive [ 25] at NCBI were included in this study (Table 2).
And there are numerous stories of nonprofit organizations trimming programs, reducing staff, or even shutting their doors as a result.
To survive, many were forced to trim programs and hastily assemble collection shows.
He said any budget cuts should first look to trimming programs "where costs have spun out of control".
