Sequencher 4.8

Category Cross-Omics>Sequence Analysis/Tools

Abstract Sequencher 4.8 is the biologist’s choice for DNA sequence assembly and analysis software.

Sequencher 4.8 features/capabilities include:

1) Sequence Editing -- Sequencher gives you the DNA sequence editing tools you need to know that a sequence is absolutely correct. You can look at your chromatogram data one sequence at a time or view multiple aligned chromatograms in both forward and reverse orientations. It lets you scroll through your aligned data or you can use Sequencer's selection tools to highlight regions of discrepancy or low quality.

2) Sequence Trimming -- Sequencher provides simple-to-use but advanced tools that help you trim poor quality or ambiguous data:

Note: Prior to executing a Trim, Sequencher displays a graphic representation of the proposed Trim which allows you to further refine your criteria.

3) Sequence Assembly -- Sequencher's intuitive controls allow you to set your sequence assembly parameters and adjust them within seconds, allowing you to assemble your DNA fragments quickly and accurately. Sequencher will automatically compare the forward and the reverse-complement orientations to assemble the best possible contigs, so you can assemble DNA sequences regardless of orientation.

Apply Sequencher's assembly tools to:

4) Support for Confidence Values -- Sequencher displays confidence and summary confidence information (if available in your DNA sequence files) in the Project window, the Sequence Editor, and the Sequence Get Info window, so you can monitor the quality of your data. You can specify cutoff ranges for your confidence values, and see those ranges by color codes.

5) GenBank Feature Handling -- Sequencher imports GenBank Features in your files (if present) and has a variety of tools to help you manage, add, or edit Features. You can import Genbank Feature keys, or designate a key for your own features. The Define Feature Key Default Style user preference lets you set up your own colors and Feature annotations, so you could distinguish introns from exons, and variants from sequencing errors for example.

6) SNP Detection -- Sequencher has several advanced tools to help you detect mutations and Single Nucleotide Polymorphisms (SNPs) in you DNA sequences. You can use Sequencher for comparative sequence alignments among a group of sequences, or to compare one (1) or more sequences to a Reference Sequence. Sequencher’s Call Secondary Peaks function analyzes all of your sequences for potential heterozygote.

You can navigate from one heterozygote to the next via the Bases view. View protein translations for both the consensus and the Reference sequences below the consensus. The Reference sequence ensures that the numbering of your SNPs is consistent from one DNA assembly to the next.

7) The Variance Table -- An advanced tool for SNP analysis and more - The Variance Table lets you sift through large quantities of sequence data so you can quickly visualize the bases of greatest interest to you. Each cell in the Variance table is linked to its original data, so you can validate or edit each putative difference directly in the Table, and have the sequence and chromatogram data updated automatically.

Once you’ve found all the differences, Sequencher provides you with a variety of export and reporting options. These are described in greater detail (see below) in the Reports (New in 4.8) paragraph.

8) Translated Variance Table (New in 4.8) -- The Translated Variance Table summarizes all amino acid differences in a selected set of samples. Because the table is linked to the underlying sequence data, it is ideal for validating mutations that result in changes to the amino acid translation and for checking expression vectors.

Unlike the Variance Table that displays matches to the Reference as blank cells, the Translated Variance Table displays matches in light grey. This enables you to see the differences in codons that still result in matching amino acids. You can even see both the Variance Table and the Translated Variance Table in Review mode, so you can precisely determine which DNA sequence changes result in protein sequence changes.

9) Restriction Mapping -- Sequencher provides a rich set of tools for generating linear restriction maps of your DNA sequence. Filter your enzyme selection by frequency, nature of the overhang, or length of recognition sequence. You can also specify particular vector and polylinker sequences to help you set up your cloning strategy.

10) Automated Analysis -- Sequencher batch processes your DNA sequence data in a way that is transparent, user definable, and recoverable, and Sequencher never jeopardizes the validity of your scientific conclusions for the sake of automation. Sequencher always gives you the final choice in your sequence editing.

Sequencher always maintains two (2) copies of your data, the edited and the originally imported data. You can undo all or a portion of your edits when you apply the Revert to Experimental Data command to a selection of sequences in your project or to a selection of bases in a sequence.

The Assemble by Name tool allows you to choose a portion of the fragment name to act as a shared identifier, or "assembly handle." Sequencher then makes the selections and names the contigs automatically. Sequencher even supports Regular Expression matching for setting up the unique IDs!

Assemble by Name is particularly helpful if you do a lot of sequencing and if you have numerous samples that are done with a standard set of sequencing primers.

11) Customize your Workspace -- You can define the default positions of your windows and Sequencher remembers your settings for format and consensus options. You can also save all your settings, including a Reference Sequence as a Project Template that can be reused.

Sequencher lets you:

12) Reports (New in 4.8) -- Sequencher’s new output Reports create printable versions of your data. The Reports provide analysis tools such as clustering of like samples in the Population Report.

The Population Report is a unique summary of the data in the Variance Table. Each Population Report consists of two (2) types of tables; one Populations table and several individual detail tables that describe each group in the Populations table.

The Variance Detail Report - provides all of the information available in Sequencher to support the Variance Table. Like in the Individual Variance Reports, a summary table lists the Variants for each sample or column. Additionally in the Variance Detail Report, a Detail Table follows the Variant Table for each of the described variants.

The details in this table include the sequence names, orientation, and base call of any data that contributes to the calling of the Variant. If confidence or chromatogram data are available, this is also included for each sequence in the table. The chromatogram data include the specifics of secondary peak contribution and an image of the chromatogram for up to six (6) tracelets per variant.

System Requirements

Macintosh Minimum Requirements:

Windows Minimum Requirements:


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