Form Bio Platform Documentation
Form Bio Platform Documentation
Sequence Alignment

Sequence Alignment

Gene Molecular Evolution

Create a multiple sequence alignment, phylogenetic tree, and calculate gene conservation

Workflow Walkthrough

  1. Navigate to the Gene Molecular Evolution workflow on the Form Bio platform. You can use the search bar to locate this workflow, or select the Sequence Alignment workflow on the left-hand side.
  2. Take a moment to review workflow inputs, outputs, and the workflow summary. Select version 1.1.1 from the dropdown menu, and click Run Workflow when ready to begin.
    3. image
  3. Currently, four starting points are supported. MSA can be created from a curated gene family, a set of orthologs, an OrthoFinder run, or from a database search. Upload the associated files or inputs pertaining to your starting point.
    4. image
  4. Tune some parameters related to the creation of the MSA, including the algorithm to use, the phylogenetic tree algorithm to use, and the sensitivity.
    5. image
  5. Take a moment to review workflow inputs and parameters, and give the workflow run a unique name. When ready to submit, click Run Workflow.
    6. image

Results Walkthrough

  1. To view the results of your Gene Molecular Evolution workflow run, first find and select your workflow run in the Activity tab.
  2. Navigate to the Files tab, and then outputs. Here, all output analysis files are nested.
    3. image

Sequence Similarity Search

Find gene sequences that are significantly similar to known query sequences

Runtime Estimates

Average = 1 hour 19 minutes

image

Workflow Walkthrough

  1. Navigate to the Sequence Similarity Search workflow. You can use the search tool at the top right corner, or find it using the Sequence Alignment filter on the left side.
  2. Select version 1.0.2 from the dropdown menu in the top right corner. You can view use cases, a summary, and inputs/outputs on this page. When ready to begin analysis, click Run Workflow.
    3. image
  3. Launcher Tabs
    1. Provide a FastA file containing the query sequence(s). Then, select the type of sequence search (nucleotide to nucleotide, nucleotide to protein, etc), the search algorithm, and the database to search.
      2. image
    2. Determine how you want to the output file (XML, HTML, etc), and tune additional search parameters depending on your chosen algorithm.
      3. image
    3. Review workflow parameters and inputs, and give the workflow run a unique name. When ready to submit the job, click Run Workflow.
      4. image

      Results Walkthrough

    4. To view the results of your Sequence Similarity Search workflow run, first find and select your workflow run from the Activity Tab.
    5. Navigate to the Files tab, then find workflow outputs under the output folder.
      6. image