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Working with core labs that use structured naming conventions to track data for individual clients, we developed the Assemble by Name strategy that has become such a powerful and popular tool for combining multiple sequencing projects into a single analysis run.
MUSCLE
MUSCLE[2], a multiple-sequence alignment (MSA) program, joins the Sequencher 5.1 family of plugins. It joins Clustal, making it the second MSA program in Sequencher’s DNA-Seq Tools. Boasting both speed and accuracy, it compares very favorably [3] to other multiple-sequence alignment programs.
Sequence Trimming
Automated DNA sequencers occasionally produce poor quality reads, particularly near the sequencing primer site, and toward the end of longer sequence runs. The sequences of clones from DNA libraries frequently contain vector sequence, polyA tails, or other unrelated sequence. Introns and primer sequence frequently flank the sequence of amplified exons. Unless removed by trimming, any of these artifacts will distort your sequence assembly and downstream sequence analysis.
Your results are important to you. Whether you work with Sanger Sequencing or Next-Gen Sequencing, you will want to compare your results with publically available data. Sequencher Connections is ideal for a quick search or a more detailed and prolonged analysis across multiple databases and with different parameters.
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