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    Release Notes

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    uriel
    The document summarizes new features in the updated version 4.1.4 of the SEQUENCHER software for assembling and analyzing DNA sequencing data. Key updates include the ability to designate reference sequences, assemble only to reference sequences, import Phred and Phrap files containing quality scores, expand the restriction enzyme list, and add a speech feature to read sequences aloud. The software is now more compatible across platforms and file formats.

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    © All Rights Reserved
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    Release Notes

    Uploaded by

    uriel
    12 views3 pages
    The document summarizes new features in the updated version 4.1.4 of the SEQUENCHER software for assembling and analyzing DNA sequencing data. Key updates include the ability to designate reference sequences, assemble only to reference sequences, import Phred and Phrap files containing quality scores, expand the restriction enzyme list, and add a speech feature to read sequences aloud. The software is now more compatible across platforms and file formats.

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    The document summarizes new features in the updated version 4.1.4 of the SEQUENCHER software for assembling and analyzing DNA sequencing data. Key updates include the ability to designate reference sequences, assemble only to reference sequences, import Phred and Phrap files containing quality scores, expand the restriction enzyme list, and add a speech feature to read sequences aloud. The software is now more compatible across platforms and file formats.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    12 views3 pages

    Release Notes

    Uploaded by

    uriel
    The document summarizes new features in the updated version 4.1.4 of the SEQUENCHER software for assembling and analyzing DNA sequencing data. Key updates include the ability to designate reference sequences, assemble only to reference sequences, import Phred and Phrap files containing quality scores, expand the restriction enzyme list, and add a speech feature to read sequences aloud. The software is now more compatible across platforms and file formats.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 3

    SEQUENCHER for Windows version 4.1.

    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.

    Introducing the Reference Sequence


    Using this feature will allow you to identify one or more of your fragments as a Reference Sequence simply by selecting the
    fragment(s), and then selecting Reference Sequence in the Sequence menu Your sequence icon(s) will be marked with an
    “R” to identify them as Reference Sequence(s).

    Assembly to the Reference Sequence


    Once you have designated your Reference Sequence(s), you can assemble them with your data fragments. Each contig may
    contain only one Reference Sequence. To increase the efficiency of an assembly that contains a Reference Sequence, under
    the Contig menu, choose the command, Assemble Contigs/Only to the Reference Sequence. When you direct your
    assembly with a designated Reference Sequence, your data fragments will only be compared to the Reference Sequences (NOT
    to each other).

    Reference Sequence Behavior in a Contig


    Within the contig editor, your Reference Sequence will be distinguished by gray lines around its bases. The Reference Sequence
    will not contribute to the consensus, and all the numbering within the contig will be relative to the Reference Sequence. Gaps
    that need to be inserted in the Reference Sequence will be numbered fractionally. For example:

    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.

    [email protected] 1 1.800.497.4939
    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.

    Phred and Phrap files


    This release of SEQUENCHER extends our support for multiple data formats with full ACE file support, the file format for Phrap
    assemblies. To import an .ACE project, do the following:

    • 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).

    Alternatively, you can import individual Phred-called sequences.

    • 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.

    Working With Restriction Enzymes


    Expanded Enzyme List
    The restriction enzymes that are available in SEQUENCHER’s mapping function have been greatly expanded. The list has been
    updated to include many of the newer enzymes.

    [email protected] 2 1.800.497.4939
    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.

    [email protected] 3 1.800.497.4939

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