The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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UPCOMING MAINTENANCE – Monday, June 29, 2015 5 AM MST through Tuesday, June 30, 2015 5 PM MST
The iPlant Collaborative will be relocating several racks of hardware containing iPlant's core services into a newly renovated data center.
Due to the nature of the maintenance, all iPlant systems and services, including any "Powered by iPlant" services, will be unavailable during this time.
Email to iplantcollaborative.org addresses will be unavailable during the maintenance as well, but will resume afterwards.

The maintenance will occur between the following days and times: Monday, June 29, 2015 5 AM MST through Tuesday, June 30, 2015 5 PM MST. 
View times in your time zone here:
  Start time: http://goo.gl/hnwizF   End time: http://goo.gl/mN7wjZ

 

Please email iPlant Support with any questions or concerns.

 

 Partial list of affected services
  • Atmosphere: Any running instance at the time of the maintenance will be suspended or stopped.
  • Discovery Environment: Any running analysis jobs will be administratively canceled.
  • Agave
  • Data Store
  • Bisque Image Processing
  • CoGe
  • DNA Subway
  • TNRS
  • www.iplantcollaborative.org
  • IBP
  • My-Plant
  • Wiki, JIRA
  • LDAP/CAS Authentication
  • User Portal (user.iplantcollaborative.org)
  • iMicrobe

 

 

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The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

EMBOSS Splitter

splitter splits one or more input sequences into smaller, optionally overlapping, subsequences. The subsequence size and overlap (if any) may be specified. Optionally, feature information will be used.

Quick Start

To use splitter, upload your input data in GenBank, Embl, or Emsembl formats.

Test Data

Input File

The input is a standard EMBOSS sequence query (also known as a 'USA', Uniform Sequence Address) with associated feature information, such as Genbank, Embl, and Ensembl formats.

  • Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> BA000025.txt

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Output File(s)

Standard EMBOSS output sequence file.

  • Expected output files: Community Data -> iplantcollaborative -> example_data -> EMBOSS -> Output -> splitter.output

Tool Source

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