1. Analysing a Nucleotide Sequence

    This example is based on obtaining a set of open reading frames (orf) from an input DNA sequence. The results of which are used to pipe into other programs for a series of analyses.
    The steps for such a workflow is as follows:
    1. Run getorf with an input sequence to obtain orfs in both translated and untranslated format.
    2. Pass the untranslated orf output into:
      1. eprimer3 which would pick the PCR primers and hybridization oligos.
      2. remap to display the sequences with resrtiction cut sites, translation and all.
      3. showorf to pretty print the untranslated orf.
    3. Pass the translated orf output into:
      1. garnier to construct the 2D structure of the translated sequence.
      2. iep to calculated the iso-electric potential of the sequences.
    4. Gather the results into the result directory.
    5. Run the workflow in a computer or server with EMBOSS-2.8.0 installed. Ask the administrator for the path and add the path to EMBOSS to your PATH variable. Other environment variables are needed such as PLPLOT_LIB and EMBOSS_DATA. Additionally, you should also have primer_core installed as it is used by eprimer3.
    6. After the workflow finishes, check the result directory for the output files.

    Draw the flow diagram below or load from the examples directory

    Analysing a Nucleotide Sequence

    Fill in the data for the program objects

    Step 1

    Step 1 a

    Step 1 b

    Step 2 and 3

    Step 2 and 3 a: garnier

    Step 2 and 3 b: iep

    Step 2 and 3 c: eprimer3

    Step 2 and 3 d: remap

    Step 2 and 3 e: showorf

    Step 4

    Step 4

    Step 5

    Step 5 a:Run workflow

    Step 5 b: Workflow executing

    Step 5 c: Workflow completed

    Step 5 d: Results directory

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Copyright © 2004 CHUA Ching Lian, Bioinformatics Institute, A*Star, Singapore.