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Home » Analyses » RNA-Seq
Over the last few years, RNA-Seq has become an immensely popular technique its own right as an adjunct to microarrays in gene expression studies.
Gene Codes has long been an innovator, investing in the R&D to develop powerful features for your DNA sequence analysis. Gene Codes developed the Assemble to Reference Sequence strategy that is widely used to speed up assembly and assign base-numbering systems and features to new data. The variance table was developed in the mid 1990's and became a key element first for forensic sequencing of mtDNA, and then for virtually all of our collaborators.
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.
MUSCLE is said to have four major steps in its alignment process. The first step constructs a distance matrix between pairs of sequences using k-mer clustering, this is then converted into a tree. The second step uses this tree to guide a progressive alignment. In the final two steps, the MUSCLE algorithm tries a number of different methods to see if it is possible to improve the tree and hence the multiple alignment.
Once the process is complete and MUSCLE has built the alignment, you will see the results as a contig within Sequencher. Use Sequencher’s tools to annotate your alignment or export your alignment and place it into a special phylogenetics program.
BWA, Velvet, Maq, GSNAP and Tablet are only the start for Sequencher. If you are sequencing mixed populations, then combine the power of reference-guided-alignment with de novo assembly. Align reads to a reference and capture the unaligned reads for further rounds of reference-based alignment or de novo assembly.
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