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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Bulk Blast 2 Sequences

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Blasting multiple sets of query and subject sequences.

Overview of tool

  • Input for this app are two directories/folders (one designated as a query folder, the other as subject folder), each folder with multiple files, each file with a single nucleotide sequence. Each file in the query folder will contain a single nucleotide sequence in FASTA format. Each file in the subject folder will contain a single nucleotide sequence in FASTA format. Each query sequence file in the query sequence folder should have a matching subject sequence file in the subject folder and vice versa. 
  • 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 generated is a blast report for each pair of query and subject sequences.

Test Data

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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 the folders testquery and testsubject from the directory above as test input folders for the query and search folder inputs in the app. Use the 'pairsist' file in this directory as the input for the pairs list. Choose any name of your choice for the output directory name. 

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 a text file named after the input files as output. For the test case, the output files you will find in the example_data directory you name in the input options. 

Tool Source for App

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