Gene Codes Corporation services

Sequencher has built its reputation on proprietary DNA sequence assembly algorithms that have set the standard in research labs across the world for over 25 years.  No other program gives you such a comprehensive set of science-driven features that can fit almost any project and get results fast. Sequencher has several different assembly algorithms as well as different assembly modes providing the flexibility to work with any of kind sequence data. With three different assembly algorithms for Sanger data,  you have complete control over the way your DNA data is assembled. The first algorithm is tuned for data the way it comes off the sequencing machine, the second algorithm lets you control how many consecutive mis-matches you will allow in your assembled data, and a third one that deals with large gaps (anything over 10 bases) with ease.

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. The ability to sequence RNA and align it prior to further analyses is a powerful but technically challenging technique. This is largely due to the fact that the powerful sequence aligners are all command-line driven. Sequencher gives you a consistent graphical user interface across its NGS algorithms and access to all the options that you would normally see on the command line.

With more than a decade of commercial availability behind them, microarrays are still a popular method of gene expression profiling despite the increasing popularity of RNA-Seq. Whether you are working with microarrays looking to re-analyse pre-existing results or trying to perform concordance studies with RNA-Seq, CodeLinker is the tool to answer all your needs. CodeLinker uses the metaphor of the experiment for each analysis or step. This means that you can experiment to get the right settings and use the right analyses to best illustrate your data and results.

The end goal of RNA-Seq analyses for many is differential expression. The best tool is Cufflinks, a suite of peer-reviewed algorithms found in Sequencher. In its simplest form, this is a four step process which takes you from re-alignment to differential expression by way of normalization. All of the steps are carefully presented through graphical user interfaces with access to command-line options but without going through the command line itself. The suite can deal with replicates and different experimental samples or conditions.

As well as its assembly algorithms, Sequencher includes not one but two multiple-sequence alignment algorithms, Clustal and MUSCLE. A multiple sequence-alignment or (MSA) is not the same as  sequence assembly so don`t be surprised if your contigs and multiple-sequence alignments look different. The algorithms which produce them are doing different tasks. An MSA, which will be your starting point for phylogenetic analysis, is created using specialized algorithms which will need to insert gaps in order to maximize the number of matching bases. One issue is that, as new sequences are added into the growing alignment, the number of gaps tends to increase in order to accommodate the new sequences. This means that alignment errors early can’t be corrected and is a problem that Clustal will be subject to. So using Sequencher to obtain the best possible consensus sequence from your sequencing run is a great start.