Sequencher

Do you ...

  • Analyze SNPs?
  • Sequence DNA?
  • Validate PCR products?
  • Assemble DNA fragments?

If you do, then consider using this month's Bioinformatics Tool of the Month: Sequencher, Software for DNA Sequencing

The purpose of this email is to introduce Sequencher to those who are not familiar with it; a software demonstration is also planned. In addition, we want to find out if people would like to use Sequencher on PCs (WIS currently only has Macintosh licenses).

Software demonstration

Shifra Ben-Dor of the Bioinformatics Unit will demonstrate Sequencher on Sunday, 31.10, at 13:00, in the Katzir Auditorium. Please join us to learn more about this tool.

Features

Sequencher's primary function is viewing DNA sequencing information and processing sequencing data; it is currently used in 28 WIS labs. A wide variety of capabilities have been added in response to user feedback over the past 13 years. Its features include:

Assembly and alignment:

  • Viewing, editing, and assembling data and chromatograms generated by DNA sequencers
  • Contig assembly to join DNA fragments into longer sequences for shotgun sequencing
  • cDNA alignment to genomic DNA sequences, even in the presence of large gaps
  • Aligning patient samples
  • Use of confidence scores for more sensitive trimming of poor-quality data

Sequence analysis:

  • Open reading frame (ORF), motif, and SNP analysis
  • Use of Reference Sequences for comparative alignments and mutation detection
  • Restriction enzyme mapping
  • Heterozygote detection when simultaneously sequencing multiple alleles
  • Multiple-frame protein translation to translate ambiguous but non-degenerate codons

Processing sequencing data:

  • Editing tools for navigating to and displaying ambiguities, disagreements, and SNPs
  • Annotating and highlighting regions of interest
  • Sequence-specific trimming for automated removal of vector or transposon sequences
  • Scalable display of individual and aligned chromatograms

For further information see the Gene Codes website: www.genecodes.com/sequencher/. You can download a demonstration version from www.genecodes.com/downloads/; it includes all features except saving, exporting, and printing.

Availability and pricing
Macintosh: The maintenance fee is $9/month. This fee is charged per computer, so a lab with Sequencher on two computers pays $18/month. A one-time fee of $10 is charged for installing the software or moving it from one computer to another.
PC: At present, Sequencher is only available at WIS on Macintosh computers, but several labs have expressed interest in the PC version. If enough labs are interested, we will a cquire the PC version as well. The maintenance fee will likely be $20/month. If you would like to use Sequencher on the PC, please contact Rhoda Frydman e-mail: Rhoda.Frydman@weizmann.ac.il, ext. 4315.

Contact information

To have Sequencher installed in your laboratory, please contact Rhoda Frydman e-mail: Rhoda.Frydman@weizmann.ac.il, ext. 4315.
For help using Sequencher, please contact Shifra Ben-Dor e-mail: Shifra.Ben-Dor@weizmann.ac.il, ext. 2470.