Release Notes
Release Notes
Release Notes
4
Stronger, Better, Faster
We are proud to present SEQUENCHER 4.1.4 for Windows. Many of the features that we have introduced will be apparent in
your everyday work. Others you will discover as SEQUENCHER assembles and performs even faster than in previous versions.
Before we could release this software to you, Gene Codes’ Quality Assurance Group and our dedicated Beta Testers thoroughly
tested all aspects of this program. The following is a list of some of the changes that you will discover as you use this upgraded
version of SEQUENCHER.
Compare to Reference
You can also create a difference report by comparing any fragment within your contig to the Reference Sequence. Select a
fragment in the contig and then Compare to/Reference Sequence under the Sequence menu. Alternatively, because the
Reference Sequence does not contribute to the consensus sequence, you can select the Reference Sequence within a contig and
compare its sequence to that of the consensus, Compare to/Consensus.
ReAligner
Within the Assembly Parameters dialog, you will find a new option, called ReAligner. This option functions after the initial
assembly is completed. The ReAligner option aligns the placement of gaps within the contig. The gaps in the contig are placed in
a way that facilitates the editing of the sequence in the consensus.
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Increased Compatibility
Cross Platform Portability
If you are a long time user of SEQUENCHER you will be pleased to learn that SEQUENCHER 4.1.4 can work with projects from
all 4.x releases of SEQUENCHER, including files created in the current Macintosh release. If you are working with older 3.x
Macintosh files, Gene Codes has supplied a converter application to enable you to work with these projects as well. As with the
SEQUENCHER 4.0.5, you will still be able import sequencing data from both Windows and Macintosh based sequencers.
• Select the ACE Project submenu item from the Import menu.
• Select a file that ends with “.ace” or “.ace.x” or (such as ace.1, ace.2, etc) - this file will typically be in the subfolder
“edit-dir”. Select the highest numbered ACE file to account for all editing and reassembling.
SEQUENCHER will automatically import and incorporate as much auxiliary data as it can, providing the auxiliary files are in
the same folder as the .ace file or arranged in the traditional Phrap assembly hierarchy (chromatogram files in a “sibling”
chromat_dir folder, PHD files in a “sibling” phd_dir folder).
• To import just the chromatogram files from the chromat_dir folder, use Import/Sequences... or Import/Folder of
Sequences... in the File menu. These fragments will have phred base calls and chromatogram data, but no quality scores.
• To import chromatograms, base calls and quality scores, use Import/Sequences in the File menu. You may select either
FASTA files from the edit_dir folder, or PHD files from the phd_dir folder. If corresponding chromatogram and .qual auxiliary
files are available, you will have imported all the Phred files and they will have the base quality and chromatogram data.
If your PHRAP assemblies reside on a UNIX workstation, SEQUENCHER can easily access this data from a shared network drive.
If you are using FTP, be certain to always transfer files in BINARY mode.
SCF Files
Newer SCF files may contain quality score data. SEQUENCHER’s support for the SCF format has been enhanced to include use
of this quality score data.
• SEQUENCHER will import quality scores present in SCF 3.x files along with chromatograms, called bases and other
experimental data.
• SEQUENCHER will also export SCF 3.0 files with quality scores.
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Setting Default list
SEQUENCHER comes installed with a default list of enzymes. In SEQUENCHER 4.1.4, you can define your own default list of
enzymes. After making your edits to the standard enzyme list in the Specify Restriction Enzymes... window, click on the
Save button. If you save the list as Default Enzymes.RST in the same folder as the SEQUENCHER application (\Program
Files\Gene Codes\SEQUENCHER 4.1.4), your custom list will become the default list, and load into the enzyme window every
time you launch SEQUENCHER.
Speech
Under the Sequence menu you will find a new item, called Speech. This will allow you to have SEQUENCHER read back
a sequence, or read bases as you type a new sequence or make edits. In addition to the new menu command, there is an
additional General User Preference, Sound, which will allow you to adjust the volume and speed of the speaker.
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