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The recipe produces pairwise alignments with different software

"Aligning sequences" appears to be a well-defined concept - in reality, it is everything but. The differences in the way aligner operate as well as what they are able to report can be radically different. Adding to the complexity even the same tool may report more or less information, various formats depending on the customization that we apply. Sometimes, certain answers can only be obtained if one were to choose to run a very specific software in a specific way.

The recipe provides code that takes two sequences (by default the 1976 Ebola genome and the 2014 Ebola genome) and generates alignments with different methods between the two viral genomes.

  1. Downloads both sequences from NCBI
  2. Uses an optimal global sequence aligner
  3. Uses a local aligner
  4. Uses a semi-global aligner

In each case the aligner is asked to produce different outputs, hence ending up with several files for each method.

Lecture

A detailed presentation that explains the steps and rationale for this recipe can be found at:

Please refer to the lecture above for study materials and additional content.

Recipe Code
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Recipe Interface
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Integer values
                        [size]
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
                    
Float values
                        [cutoff]
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
                    
Text box
                    [sra]
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
                    
Dropdown menu
                    [color]
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
                    
Check box
                    [validate]
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
                    
Upload Field
                    [file]
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
                    
Pick Data
                    [data]
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
                    
Radio Buttons
                    [species]
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
                    
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