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 – TUESDAY, JUNE 28

The Discovery Environment will be unavailable on Tuesday, June 28, from 8:00 AM to 5:00 PM MST (check your local timezone here) while version 2.7 is deployed. All currently running analyses will be canceled; please plan your analyses accordingly.

Other affected systems are the Data Store (offline for regular maintenance), Atmosphere (instances will continue to run but new instances will not be launchable), BisQue (unavailable due to Data Store maintenance), and TNRS (unavailable while a small update is applied).

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We apologize for any inconvenience. If you have any questions or concerns, please contact support@cyverse.org.

 

 

 

 

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EMBOSS trimseq

trimseq reads one or more sequences and writes the same sequences out, but removing any regions at the start and / or end that contain unwanted characters. These include gap characters (where occur the sequences have been aligned), X's and N's (in nucleotide sequences), *'s (optionally) and (optionally) IUPAC ambiguity codes.

Quick Start

To use trimseq, upload your input data in fasta format.

Test Data

Input File

  • Test input in fasta format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> untrimmed_myseq.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

Standard EMBOSS output sequence file. Trimmed sequence can be in fasta format by default.

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

Tool Source

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