Introduction
Welcome to stackPACKTM v2.2. The stackPACK clustering system allows rapid clustering,
alignment and analysis of ESTs as well as full-length sequences by providing sophisticated gene indexing capabilities
that go well beyond other clustering and assembly tools.
A web-based interface is provided with stackPACK.
This interface gives access to the following programs:
WebPipeTM:
Project creation and initialization of the clustering process.
WebProjectManagerTM:
Project manipulation, addition of new data and management.
WebProbeTM:
Results viewing.
WebReportTM:
Output reporting for download and evaluation.
The following stackPACK documentation is available:
Detailed
user manual, with links available from every page of the
interface.
Naming
conventions used in the stackPACK interface.
Input
data format descriptions.
Command
line user manual.
A brief guide to the interface, provided below.
How to use the
WebPipe (more...)
- Click on WebPipe in the menu bar.
- Enter details as follows:
- Project Name - Enter a brief one-word project name.
- Project Owner - Enter your e-mail address here to be
notified when your data has been processed.
- Project Description - Enter a project description.
- Select the sequence data format from the pop-up box.
- Click on the "Next" button.
- Use the browse button to specify the name and complete location of
the input data file or quality file.
- Click on "Upload" to begin the clustering pipeline.
How to use the
WebProjectManager (more).
- Click on WebProjectManager in the menu bar for a list of the
various projects.
- If desired, restrict the project list by filtering by project
name, owner or description.
- Click the project name in order to display a summary
report.
- Select a project by ticking the box next to the project name,
and:
- Click "Delete_Project(s)" to delete one or more projects.
- Click "Add_Sequences" to incrementally add new sequence data to
an existing project.
- Click "Edit_Description" to edit a project description.
How to use the WebProbe
(more).
- Click WebProbe in the menu bar.
- Enter the project name and owner, or enter a portion of the project name and click "Search" to be presented with a list of options.
- Query WebProbe in one of the following ways:
- by accession number: enter a sequence, cluster, contig, consensus or clonelink accession number
and click "View".
- for clusters with potential alternate expression forms: click "Alternates_List".
- for a summary report: click "Summary".
How to use the WebReport (more).
- Click on WebReport in the menu bar.
- Enter the project name and owner, or enter a portion of the project name and click "Search" to be presented with a list of options.
- Choose the type of report you wish to generate.
- Click on the "Next" button to select the report options.
- Click on the "Export" button to generate the report.
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