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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Generate detectability cartoons for syntenic features

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Generate detectability cartoons for sytenic features

Overview of tool

  • This app parses a standard blast report based on user defined criteria. Please note: default is to parse the blast report using bitscore cutoff of 29.5. This cutoff is based on the threshold limit for identifying syntenic noncoding regions (eg., Conserved Noncoding Sequences). 
  • The main input for this tool is a directory of blast output files.
  • The app also takes as input a pairs list, a tab delimited file of the format: "queryfilename,chr,start,stop,strand,gene,orth,subjectfilename", with each line referring to one of the files in the query folder and to its corresponding subject file in the subject folder. The chr, start, stop, strand and gene info in the pairs list refer to the genomic location of the feature which is being blasted. (This is in the context of when you are trying to identify the presence of a feature in its expected syntenic position.
  • The output of this app is a file of the format: "queryfilename,"\t",subjectfilename,"\t",gene,"\t",orth,"\t",Detectable (Y/N) for each feature.

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> SyntenyFinder.

Input File(s)

Use pairslist from the directory above and sampleParse from the directory testsample as test input.

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)

Expect the same file name as the output file name you entered before submitting the app. 

Tool Source for App

  • There is no additional source for this app. The script for this app was built using Perl.
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