This article is translated by China Science Software Network
Sequencher sequence analysis software
Sequencher is a DNA sequence collection and analysis software. It works with all automated sequencers and is known for its fast Contig assembly, friendly editing tools, and superior technical support. Sequencher is used by life science researchers in different DNA sequence analyses, including genetic recombination, mutation detection, forensic human identification, and taxonomy.
Sequence editing
Sequencher provides you with a DNA sequence editing tool that lets you know if a sequence is completely correct. You can view chromatogram data at a rate of 1 sequence/time, or observe multiple alignment maps in both forward and reverse directions.
It can be easily and quickly scrolled through your matching data, and you can also highlight areas with differences or low quality through Sequencher's option tool.
Sequence finishing
Automated DNA sequencers occasionally result in low quality reads, especially near the sequence primer sites and at the end of the long sequence. The cloned sequence of the DNA library typically includes a vector sequence, a polyadenylation tail or other unrelated sequence. The intragenic region and primer sequences are often located on the side of the expanded exon sequence. These artifacts will distort your sequence set and subordinate sequence analysis unless you remove them by adjustment.
Sequencher provides easy-to-use but powerful tools that can help you remove low-quality or fuzzy data:
Trim Ends can remove misleading data from the end of a sequence fragment
Trim Vector can delete the exact sequence data at the end of the destruction sequence
Trim to Reference excludes the end of the combined reference sequence.
Priority execution of the adjustment command, Sequencher shows a graphical representation of the proposed finishing, which can further improve your standards.
Sequence collection
Sequencher's intuitive controls allow users to set their own sequence set parameters and adjust them in seconds, while allowing users to quickly and accurately combine DNA fragments. Sequencher automatically compares the forward and reverse complement orientations to assemble the most likely contigs so you can assemble DNA sequences without regard to direction.
Sequencher's universal collection tool can be used to:
Comparative gene variants and reference sequences
Determining vector structure
Bring together the viral and bacterial genomes
Clustering thousands of sequence numbers from a cDNA library
Combine cDNA and genomic sequences
Create a primary map
Support confidence value
Sequencher displays the trusted and overall trusted information in the project window, sequence editor and sequence information acquisition window (if it exists in your DNA sequence file) so you can monitor your data quality very easily. You can even specify a cutoff for your confidence value and view these variations in color code.
Gene bank feature manipulation
Sequencher enters GenBank Features into your files and provides many tools for managing, adding or editing features. You can enter Genbank Feature keys or identify your personal characteristics. Define Feature Key Default Style defines the default form of the user. Users are more willing to let you set your own color and feature annotations, so you can distinguish introns from the exons and find the sequence errors.
SNP detection
Sequencher has some powerful tools to help you detect DNA sequence variations and SNPs. You can use Sequencher to compare sequence corrections in a set of sequences, or compare one or more sequences to a reference sequence. Sequencher's call to the secondary peak function analyzes the potential heterozygote of all your sequences. You can easily control strictly defined heterozygotes.
You can move from one heterozygo to the next; just click the space bar in the Bases navigation. Browse the protein conversion of consensus and reference sequences. The reference sequence ensures that the number of your SNPs is consistent with the next DNA set.
Variance table
Powerful SNP analysis tool
There is now a very simple way to compare DNA sequences or overlap consensus sequences and find out all the differences in these sequences. These instructions can be done with just a few keystrokes. The variance table allows you to filter out interesting content from a large amount of sequence data. Each cell in the variance table is linked to the original data, so you can easily verify or edit each hypothetical difference directly in the table and automatically obtain sequence and chromatogram data. If you find all the differences, Sequencher offers you a variety of input and output options.
Conversion variance table
The conversion of the variance table summarizes the amino acid differences for all selected samples. Because this table is linked to hidden sequence data, it is an ideal validation variation tool that can lead to amino acid conversions and check vector changes.
Unlike the variance table, its display is not combined with blank cells but with light gray. You can see the difference in codons and lead to the pairing of amino acids. You can even see the browsing mode of the two tables, which can decide whether to convert the DNA sequence into a protein sequence.
Restriction map
Sequencher provides a number of mapping tools for managing the linear programming of DNA sequences. The choice of enzyme is filtered by frequency, nature or length of the known sequence. You can also distinguish between special vector and multi-joint sequences to set up your clone plan.
Automatic analysis
The Sequencher batch uses an easy-to-understand, user-defined method to process your DNA sequence data. And Sequencher will never damage the validity of your scientific conclusions. Sequencher also gives you the ultimate choice for sequence editing.
Sequencher saves you two types of data backups, edited and raw input data. You can undo all or part of the edit when you convert the experimental data instructions.
The naming tools collection allows you to select a portion of the clip name as a shared identifier or collection handle. Sequencher can automatically select and name contigs. Sequencher even supports regular expressions and sets unique IDs for matching!
For example, by clicking the button, you can convert 90 files, 45 pairs of forward and reverse sequences, into 45 contigs named after Patient IDs. Changes to the sequence collection parameters reassemble the fragments, and you can record your sequence name by cloning the ID, date, primer, or any other feature.
Name collections are very helpful for dealing with large numbers of sequences. Its role also includes:
Sequence processing of MHC and identification and study of mitochondrial genes
Candidate Gene Analysis of PCR Products
Monitoring viral genome sequences and tracking anti-linked vaccines or antiviral drugs
Customize your work location
You can define the default location of the window, and Sequencher can remember the formatting and coordination options. You can also save all your settings, including a reference sequence as a project template, and reuse it to save analysis time!
Use subtitles that are prominent and defined by the theme
Remember the size setting between the two parts
Choose the best window layout for your work and save them
Customize how your project window is displayed
report
Sequencher's latest output reporting feature creates a printed form of data. The report provides some analytical tools, such as a sample set of demographic reports.
The population report is a unique summary of the variance table data. Each population report consists of two tables, a demographic table and individual detail tables, each of which describes each group.
The Variance Detail report provides all the information that Sequencher has to support the variance table. For example, in the Independent Variance Report, the summary table lists the variances for each sample or column. Moreover, in the variance detail report, a detail form is attached to the variance table. The details of the form include the sequence name, orientation and basic requirements of any data. If confidence or chromatogram data is present, these should also be included in the sequence table. These chromatogram data consists of a secondary vertex composition and a chromatographic image of six tracelets per variance.
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