My Account | My Wishlist | My Cart | Online Ordering
Email info@licor.com
e-Seq™ Software
Automated and Accurate Sequence Analysis Software
e-Seq™ Software
e-Seq is LI-COR's Windows-based DNA sequencing software that maximizes both connectivity and sequencing automation. e-Seq controls electrophoresis, sequences electrophoresis image files, produces reports for database submission, and makes it easy to connect the 4300 System to your network.
e-Seq™ Software Details
Click any of the topics below for more information
Automate Data Collection
Longest Reads, Superior Accuracy
Bi-Directional Sequencing
Quality Values with Every Base Call
Sequence Alignment
Automate Data Collection
[Back to Top]Let e-Seq™ Automate Your 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.
Longest Reads, Superior Accuracy
[Back to Top]
[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.
[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
[Back to Top]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.
[RIGHT] Schematic of bi-directional sequencing on a double-stranded template.
Quality Values with Every Base Call
[Back to Top]
[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.
[ABOVE] e-Seq has a quality value overview window that shows quality values by base position for an entire sample
[RIGHT] 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
[Back to Top]
[LEFT] 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.
Click here to learn more about the AlignIR™ software.
Specifications
Computer System Requirements
- Microprocessor:
500 MHz Pentium II - Operating System:
Windows® 95, 98, NT, 2000, XP, Vista - RAM:
128 MB - LI-COR DNA Analyzer:
Model 4300 or Model 4200.
Capabilities
- Accessibility:
e-Seq™ has secure communication (TCP/IP) with the 4300 through direct connection, network, or via the Internet. - Automated Lane Finding:
e-Seq automatically finds lanes with high accuracy. - Base Calling:
e-Seq features extended base calling with typical read lengths of 1000-1200 bases on 66 cm gels. Base calling is performed automatically using either a 'normal' or 'heterozygote' mode. - Quality Values:
The e-Seq Software creates quality values at all base positions. Quality values for a sample can be viewed in a graph and exported directly to PHRAP or other analysis programs. Quality values can also be viewed side-by-side with curve and image data in various color-coded formats. - PHRED/PHRAP Compatibility:
e-Seq automatically creates Phred-compatible curve files for base calling and quality value generation. The e-Seq base caller also produces a file comparable to PHRED (phd) that can be imported directly into PHRAP for assembly. - Image Display:
Real time display of raw image data in a format similar to autoradiograms. - Post-Sequencing Actions:
Following base calling, samples can be automatically transferred for further analysis. Examples of automated post-sequencing actions include: Exporting sequencing data in various data bank file formats.
Exporting sample and curve files.
Exporting quality value tables.
E-mailing data in various formats.
Aligning and assembling sample files (requires AlignIR Software)
- Multiple Instrument Control:
A single computer with e-Seq Software can control any number of instruments. To start a run, e-Seq sends run parameters to the instrument. Server software in the 4300 takes over to finish the run. Since e-Seq is not needed during the run, the computer can be used for other tasks. - Data Formats:
Available data formats for each sample include TIFF image, SCF curve, PHRED compatible curve, phd.1 file, quality value graph and numerous text formats compatible with standard databases. - Image and Sample Galleries:
Galleries are used for organizing projects and editing data. Gallery functions allow projects containing numerous samples to be opened and viewed simultaneously. TIFF images produced using LI-COR Base ImagIR™ Software can also be imported into galleries for compatibility with previous LI-COR systems. - Sample Sheet Importing:
Sample names can be imported in a number of standard file formats.
Related Products
Reagents and Accessories
