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Production of the Model 4300 has been discontinued as of January 1, 2014.
Service and support may become limited. Please contact your local sales office.

e-Seq Software

Automate Data Collection

Let e-Seq™ Automate Your Data Collection

e-Seq data collection

Server software in the 4300 instrument controls electrophoresis and stores data on its internal hard disk. When runs are started from e-Seq software, the 4300 takes control, starts electrophoresis, and collects image data. One computer can control multiple instruments. The computer running e-Seq is not needed during electrophoresis and can be used to perform other tasks, such as data analysis, office computing, starting runs on other instruments, etc.

Electrophoresis image data from runs are stored on the 4300's internal hard disk. When a finished run is opened with e-Seq, image data are automatically transferred to the computer and for base calling.

Automated Base Calling

LI-COR's e-Seq software uses a Sequencing Wizard to set up automatic base calling. The Sequencing Wizard makes it easy to enter sample and lane loading information. During the run, the Sequencing Wizard automatically finds lanes with high accuracy and starts calling bases.

After the sequencing, e-Seq's Sequencing Wizard can perform post-sequencing tasks like automatic data transfer and analysis. The Sequencing Wizard can automatically align or assembly sequence data (requires LI-COR AlignIR™ software), export curve files, export files in standard sequence database formats (GenGank, etc.), and more. Files can also be submitted for BLAST searches using automatic e-mail features.

e-Seq automated base calling

Longest Reads, Superior Accuracy

3D plot of image data

[ABOVE] A 3-dimensional plot of image data near base 1100. For increased accuracy, e-Seq analyzes band morphology during automatic lane finding and base calling, rather than just analyzing an intensity trace through the center of the band.

e-Seq uses an advanced base calling algorithm that trains itself and adapts to the data as analysis progresses. Analysis of 3-dimensional, high resolution image data extends read lengths up to 1000-1200 bases per sample with 99% accuracy at 1000 bases.

e-Seq accuracy graph

[ABOVE] Average percent accuracy at each base position for 2215 sample files in a genome project. Samples represent 2.89 million bases. Data courtesy of the GENOSCOPE National Sequencing Center, EVRY, France.

Bi-Directional Sequencing

LI-COR's Simultaneous Bi-directional Sequencing (SBS™) reactions produce over 1000 bases from each end of a double-stranded template (4300L). e-Seq keeps track of forward and reverse samples with customizable naming conventions. In a single run, e-Seq can completely sequence both strands of most PCR products. After sequencing, e-Seq can automatically export forward and reverse sequences to LI-COR AlignIR software for alignment. Sequences can be immediately confirmed, making it easy to identify a heterozygote mutation sequence.

Schematic ofbi-directional sequencing

[ABOVE] Schematic of bi-directional sequencing on a double-stranded template.

Quality Values with Every Base Call

Quality value calculations

[ABOVE] Quality value calculations were validated by comparison to PHRED software for a large data set in a genome project.

Quality Values Comparable to PHRED

Each base call includes a quality value that gives the error probability for the call. e-Seq quality values are similar to those calculated by PHRED sequencing software. LI-COR sample files are compatible with PHRED software for base calling and quality value generation. Sequence files generated by e-Seq can also be imported directly into PHRAP for assembly.

Integrated Quality Values

Quality values are integrated into e-Seq operation. Edit windows show image, curve and quality values side-by-side, making it easy to examine low quality base calls. The average quality value of sequence data for a sample can be used as a threshold to determine whether a sample is included in assemblies or reports.

Quality value overview window

[ABOVE] e-Seq has a quality value overview window that shows quality values by base position for an entire sample

e-Seq sample view window

[ABOVE] e-Seq's sample view window shows image, curve, and quality value data side-by-side. Green quality value bars are quality values above 40, and blue quality value bars represent quality values between 30 and 40. The numerical quality values can also be displayed instead of bars. Sequence data can be edited directly in the sample view window, making it easy to find and edit individual base calls that have low quality values.

Sequence Alignment

AlignIR assembly software

[ABOVE] After sequence data are automatically aligned or assembled, data and the consensus sequence can be viewed in AlignIR's detailed sequence window. Base calls are linked to raw data so that double-clicking any base position displays an edit window showing image, curve and quality value data.

When LI-COR AlignIR software is installed, it is tightly integrated with e-Seq operation, providing an automated solution for sequencing and assembling samples all in one step. e-Seq can automatically create a new project in AlignIR, add sequenced sample files to the project, and prompt AlignIR assemble or align the samples. AlignIR also has many powerful tools to find and edit ambiguities, including color-coded quality values that make it easy to quickly edit low quality base calls.

Automatically Aligns Bi-directional Reactions

After e-Seq calls the forward and reverse sequences from bi-directional reactions, both sequence files can be automatically transferred to AlignIR to generate a consensus sequence. AlignIR's unique alignment software automatically inverts and aligns bi-directional samples. Raw data for both forward and reverse reactions are easily displayed when editing the consensus sequence.

Learn More about the AlignIR™ software.

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