DNA* - Products - Lasergene

SeqMan Pro

Sequencing Manager, Sequence Assembly, Contig Management, and SNP Discovery

» Printable PDF overview for SeqMan Pro

» View a video tutorial of SeqMan Pro

SeqMan enables you to assemble fragment data from sequencing projects of any size - from a few fragments to hundreds of thousands of fragments - at the push of a button. It also removes unreliable data, including poor quality ends, sub-minimal length reads, and vector and contamination host sequences in a single pass, then assembles the trimmed data and calls the consensus.

SeqMan provides two different assembly methods: the Classic assembler, and the Pro assembler. The Classic assembler should be used when: 1) your data does not contain repeated sequences; 2) you do not use vector trimming; or 3) you want to reproduce an assembly made from a previous version of SeqMan. In general, the Pro assembler should be used when your data is: 1) large; 2) contains repeated sequences; 3) has noisy ends; or 4) is being used for SNP analysis. The addition of the new SeqMan Pro assembly algorithm provides Lasergene with the tool necessary to assemble bacterial size genomes using 454® Life Sciences' pyrosequencing technology.

SeqMan uses DNASTAR's unique trace quality evaluation method to call the most accurate consensus sequence possible. This robust algorithm is so good it reduces the depth of coverage needed for accurate sequence determination, yielding spectacular savings in time and effort. A Maximum Expected Coverage (MEC) feature allows users to select the depth of coverage for an assembly and to visually identify areas where the coverage exceeds the selected level. SeqMan also uses dual-end sequence data when available to group and order contigs, allowing you to fill gaps quickly with minimal additional sequencing efforts.

To evaluate the assembly, a single alignment window allows you to view key aspects including

Two consensi for the same contig, called by different methods
Multiple sequences and their underlying trace data
The six-frame translation
Candidate SNPs
Sequence and consensus conflicts

This alignment window also enables you to locate and manipulate any nucleotide, SNP or fragment sequence and evaluate edited consequences. Once you have your contigs, you can simply BLAST* them against NCBI's data to gather information already known about related sequences.

Reads in most popular formats directly
Download sequences directly from NCBI* using accession numbers, BLAST or text searches
Add multiple sequences via drag-and-drop, the Add Sequences menu option, or use a file of filenames
Import, Edit and Export Phrap Assemblies
Add few or up to hundreds of thousands of sequences to an assembly project
Export sequences and consensi as individual or multi-sequence files in most popular formats

Remove contaminant sequences such as vector and E. coli automatically
Trim poor-quality trace data automatically using trace quality evaluation
Utilize a backbone sequence to guide assembly
Customize assembly parameters for your own data sets
Set a minimum length parameter to exclude shorter sequences
Choice of 2 assembly methods to use depending on the project size
Set Maximum Expected Coverage value to monitor depth of coverage

Use the trace quality evaluation method to achieve the most accurate consensus possible
View multiple consensus sequences, sequences, traces and six-frame translations aligned in a single window
Compare consensus sequences generated by trace evidence, majority and Phrap methods
Detect SNPs and conflicts
Resolve conflicts automatically or interactively
Merge contigs automatically or interactively
Recover trimmed data to join contigs
Force particular bases or sequences to be used for the consensus
Group and order contigs using dual-end data automatically or manually
Insert, delete or change bases and gaps in the consensus or input sequences
Reintroduce trimmed data easily and immediately view the effects on the consensus
Display 454® assemblies in Flowgrams

The new Primer Walking feature in SeqMan identifies weak coverage and sequencing gaps and helps you design sequencing primers to cover these regions
Design sequencing primers that extend upstream and downstream from an existing contig and walk into a region with weak or poor representative trace data
Complete user control over the coverage parameters including the minimum sequence coverage, base pair limitation from ends and whether the user wants to improve coverage on either or each strand

Assemble Sanger and Next-Generation sequence data (454®)
Perform iterative assemblies
Include sequencing data in formats such as ABI, AB1, SCF, Fasta, Phred and 454®
Assemble against a backbone template or use raw sequencing data
Utilize the Pro Assembler method for data sets that include repeated sequence.
For direction with specific assemblies, please review the SeqMan Help menu, or contact us.

Add sample sequences to a project and select a reference sequence against which to compare all others for variation
Automatically analyze aligned sample sequences to identify and highlight bases that are probable SNPs
Discover homozygous and heterozygous SNPs
Confirm or reject that bases are actual SNPs
Generate SNP reports that enable further genetic analysis of the sequence sample population

* Requires Internet Connection

* 454 is a registered trademark of the 454 Life Sciences Corporation

» Printable PDF overview for SeqMan Pro

» View a video tutorial of SeqMan Pro