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Genecodes 发布 Sequencher 4.10.1
2010-05-08  广州博脉
Sequencher 是 DNA 序列分析的工业标准软件。它可以和所有的自动序列分析仪一同工作,并且因为它的极速 Contig 组装、很短的学习曲线、用户友好的编辑工具,以及卓越的技术支持而众所周知。从差不多 15 年前释出第一个版本到现在,Sequencher 在每个基因专业和制药公司中都应用与于序列分析任务,同时在全球超过40个国家里为数众多的学术和政府实验室中使用。Sequencher 被生命科学研究者们使用于许多不同的 DNA 序列分析应用方面,包括基因重组、突变检测、法医的人体辨别,以及分类学等等...
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Sequencher 详细介绍请点击: http://www.pomine.com/show_software.aspx?pName=Sequencher
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Sequencher 4.10.1 Release Notes
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What’s New
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* Option to Compute Consensus by Confidence
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There is a new method that can be chosen for computing the bases that make up the consensus string. Consensus by
Confidence uses the base with the highest confidence score in the column to use as the consensus base.
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* Consensus line shows confidence shading
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When Consensus by Confidence is used, the consensus line can show confidence shading.
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* “Create New Sequence from Consensus” includes consensus confidence scores.
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This is only applicable if you have computed the consensus using the By Confidence method.
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* Contig Coverage Graph
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A new version of the Overview shows the depth of forward and reverse coverage as a histogram.
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* Generate a Shuffled sequence
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With this new command, bases of a chosen sequence are randomized to create a new sequence with the same composition but a different order.
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* Frequency Histograms and Tables
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Nucleotide frequency information is now available as a report. You can generate tables or a histogram.
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* New Import Formats
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Three major formats have been added to the extensive set currently available. These are FastQ, FastA aligned, and Contig Express projects.
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* Support for Contig Express project files (the assembler from VectorNTI)
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For those of you who have legacy projects assembled with ContigExpress (file extension .cep), you can import those projects into Sequencher, including sequence bases, names, contigs, electropherograms, features, confidence scores, base edits (including insertions and deletions), and comments.
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* Consensus by Confidence in the Variance Table
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When the Compare Consensus to Reference command is used, you see Confidence Range colors in the cells of the table where there are variant bases.
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* New Difference Column in the Variance Table
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A new column containing the total number of differences has been added to a number of the Variance Table reports.
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* Sort by Handle
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A new option to sort “by Handle” has been added to the Contig Editor Overview.
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* New AppleScript commands Get and Retrieve project item values
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New AppleScript commands have been added to Get and Set labels and comments on any fragment, contig, or refrigerator in the Project Window. Comments on the Project can also be accessed through Get and Set commands in AppleScript.
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* New AppleScript commands to access whether an item is Selected
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New AppleScript commands have been added to Get and Set the Selection state of an item.
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What’s Improved
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* Multiple Feature Listings
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The ability to open the Feature Listing has been extended from one sequence to a number of sequences at the same time.
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* Chromatograms on the Variance Detail Report
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It is now possible to set the scaling of chromatograms in the Variance Detail report.
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* Scroll Wheel enabled in more dialogues
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The Scroll Wheel on a mouse now allows you to scroll vertically through the lists in the “Assemble Interactively” dialogue.
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* Sort Project Windows by column
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Project Window columns may now be sorted in an ascending or descending order for any column.
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* Improved support for file extensions on Apple’s “Snow Leopard” operating system
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We addressed the change that Apple Computer introduced so that all the correct file types are visible in the Open Project dialog, including files ending with .spf, .SPF, .Spr and those with allowed Apple “TYPE” and “Creator” codes.
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* Trim Log File
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There is a new command to assist you in navigating to and opening the log file.
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* More “Don’t Show Again” checkboxes
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At the request of users, more warning dialogues have been given a “Don’t show this message again” checkbox.
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* Sequence trimming is much faster
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Ends trimming and vector trimming are now ubstantially faster operations, especially on large data sets.
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* Improved “Snow Leopard” compatibility (Macintosh)
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We addressed changes that Apple Computer made which affected file type recognition as well as a change that affected Clustal.
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* Improved File Lists on Macintosh
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We addressed an issue so that ACE and CAF files are now enabled and selectable in the file lists when importing ACE and CAF projects.
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* In Assemble by Name, more room for Advanced Expression
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The Advanced Expression type-in box has been made wider to accommodate longer advanced expressions for complex naming conventions.
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* Unusable characters in file names are detected on Windows
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We catch and handle a problem that was seen primarily on non-English systems on Windows. Unrecognizable characters in the full path name of a file are detected and tell you what needs to be changed for import or export.
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* “Lost” user preferences have been fixed
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An issue has been fixed where some of the User Preferences could get lost. One manifestation of this was that you might get asked to register your copy of Sequencher over and over again.
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* % Quality for Contigs
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A contig will have a % Quality value when Consensus by Confidence is in use.
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* Increased number of bases trimmed in Vector contamination
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The limit of bases trimmed in Vector contamination has been increased to 99 at each end.
 
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