sequencher4.5序列拼接软件使用说明

生物圈http:///Tour Guide for Windows and Macintosh Introduction

SEQUENCHER has been developed to work with a wide range of sequencing

applications. For example, SEQUENCHER can be used to:

Create assemblies for shotgun or EST sequencing projects Edit contigs while viewing all relevant trace data Assemble multiple sequences to a user-defined Reference Sequence Detect and annotate polymorphisms Align cDNAs to their genomic sequence using the Large Gap algorithm Discover heterozygous peaks Create difference reports for SNP discovery Display restriction maps, ORF maps, protein translations Automatically trim poor quality and vector sequences

Macintosh and PC Support

SEQUENCHER is available for both Macintosh and PC platforms. The demo CD provides software for both environments.

Unlimited Trial

With the SEQUENCHER demo, you can use your own data and enjoy an unlimited evaluation period. The only functions not available are copying data to other

applications, saving, exporting, printing, and reporting. Some sample data have been included to get you started, but once you have tried SEQUENCHER with the sample files, please try using your own data so you can see precisely what SEQUENCHER can do for you.

What You Will Learn in This Tutorial

The purpose of this tutorial is to guide you through SEQUENCHER‘s core assembly and editing functions. Additional application-specific tutorials are included on your CD in PDF format. In this tutorial, you will

1. Install the SEQUENCHER demo

2. Create a new project

3. Import data

4. Trim sequences

5. Assemble a contig

6. View contig assembly

7. Edit assembled chromatograms

8. Find heterozygotes

9. Work with a Reference Sequence

10. Translate sequences to amino acids

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11. Annotate a sequence

12. Create a Variance Table and Report

13. Create a Translated Variance Table

14. What else can I do with SEQUENCHER? http:///

Once you have mastered these techniques, you will be ready to explore

SEQUENCHER ’s other powerful features.

Conventions Used in this Guide

Menu items or keys that you are to select are in bold. The purple text provides step-by-step instructions for running through the tour guide and the black text provides additional information. Greater than symbols define menu > submenu commands. Before you start

Check that you have the appropriate hardware and disk space.

Additional Requirements will vary with your project.

MACINTOSH RECOMMENDED REQUIREMENTS:

10.3.9 and higher 512 MB RAM 150 MB hard disk space

WINDOWS MINIMUM REQUIREMENTS:

Windows 2000 and higher 512 MB RAM 150 MB hard disk space

1. Install SEQUENCHER Demo

Insert the demo CD into your machine. Double-click on the Sequencher 4.9 Demo installer icon.

The installer will create a Sequencher 4.9 Demo folder in your Applications (Mac) or Program Files > Gene Codes (Windows) folder.

2. Create a New Project

Launch SEQUENCHER by double-clicking on the Sequencher Demo icon.

On your Macintosh, this will be in the opened Sequencher Demo folder. On a

PC there is a Sequencher Demo icon on your desktop.

When SEQUENCHER is launched, a dialog will alert you that you are running in Demo Mode. After you hit the OK command button on the alert dialog,

生物圈http:///SEQUENCHER will present you with an empty Project window. This is where you

import, manipulate, and display sequence fragments and assembled contigs.

New Project Window

3. Import Data

To import data, select Import > Folder of Sequences... from the File menu.

Browse to the Applications (Mac) or Program Files > Gene Codes (Windows)

then Sequencher 4.9 Demo > Sample Data > Demo Sample Data > Demo

Sequences folder.

Click on the Choose (Mac) or OK (Windows) button at the bottom window.

When prompted to import the 9 files, select the Import All Files in Folder

command button. The Project now contains the 9 sequences.

Imported Sequences

These imported files, with their associated quality scores, are just one example of the wide variety of file types SEQUENCHER accepts for import. Note that the Quality column displays the % quality for each of the imported sequences—the percent of bases that are above the low quality threshold as set in the Confidence User

Preference pane.

4. Trim Sequences

SEQUENCHER has tools that allow you to trim imported sequences based on several different criteria: ambiguous data, data that have low confidence scores, or data

contaminated with vector sequence. The trimmed data are fully recoverable within the SEQUENCHER project. To trim the low confidence sequence:

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http:///From the menu bar, choose Select > Select All to highlight all sequences if

they aren’t already highlighted.

From the menu bar, choose Sequence > Trim Ends... SEQUENCHER displays the Ends Trimming window for the default trimming parameters.

SEQUENCHER recognizes poor quality sequence based on a number of criteria. The confidence score, provided in these samples, is one of the most sensitive. Increasing the stringency of the trim criteria further increases the quality of your data.

Select the Change Trim Criteria button. Uncheck all but the three criteria checked below, and adjust the values of the

two confidence trims to match.

Click OK to return to the overview for Ends Trimming.

The Ends Trimming window displays how much poor quality data will be trimmed based on the defined criteria. You have the additional option to individually deselect a fragment for trimming on …… 此处隐藏：18836字，全部文档内容请下载后查看。喜欢就下载吧 ……