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An in-house program called QUALSCREEN was used to quality clip the ends of sequence traces.
The ends of sequence identity were determined based on BLASTN results.
Hence, we suggest that the optimization of program parameters and trimming of low-quality bases at the ends of sequence reads might improve the assembly output significantly.
ESTPiper first invokes the commonly used LUCY program [ 8] for vector removal and to trim low quality regions at both ends of sequence reads.
It is perceivable that many gaps could be closed by designing primers at the ends of sequence contigs and using them for direct sequencing on the BAC clone.
Similarly, small gaps or mismatches that often occur at the ends of sequence tags can interrupt a match, resulting in a minimum loss of 10 nucleotides in the match alignment.
Similar(45)
Furthermore, because it is a local alignment approach, it was expected to trim the ends of sequences that were sufficiently different from their template.
Autapomorphic insertions and ends of sequences were removed from each alignment.
Prior to alignment, all sequences were trimmed to remove low-quality bases at the 5′ and 3′ ends of sequences.
We wanted to assess the correlation between the locations of the 5' ends of sequences deriving from opposite strands.
Allowing for the possibility of low quality reads at the ends of sequences, we evaluated read quality using Galaxy.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com