Emboss transeq
The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
EMBOSS transeq
Description
transeq reads one or more nucleotide sequences and writes the corresponding protein sequence translations to file. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames. The translation may be restricted to specified regions, for example, corresponding to the coding regions of your sequences. It can translate using the standard ('Universal') genetic code and also with a selection of non-standard codes.
Quick Start
To use sixpack,
- upload your input nucleotide sequence in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
- Choose your option, such as genetic code table
- launch your job
- Resource: More information on input sequence feature and format could be found at http://www.bioinformatics.nl/cgi-bin/emboss/help/transeq
Test Data
Input File
The input can be in most sequence format, such as fasta, gcg, GenBank, Embl, and Ensembl formats.
Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> test_trans.fa
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: transeq_out.fa