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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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/testsample/blastoutput/.

As an example, here are two blast reports of a feature associated with AT1G11400 to each of two Brassica orthologs.  

For this example, bitscore was set as the filter type and a value of 29.5 as set as the threshold of detectability. In the blast reports of Bra16837, there was only one hsp, with a bitscore of 27.6. Since this value is lower than out threshold of detectability, the feature was classified as  'N' for not detectable in the vicinity of the Bra16837. In the case of the other otthologs, there is one HSP of bitscore 37.2 greater than the threshold value, so the feature is classified as detectable (Y) for this ortholog. The parsed blast report indicates these calls (highlighted below). 

Input File(s)

Use the folder blastouput from the directory above as test input folder for the blast report folder input in the app. Use the 'pairsist' file in the main SyntenyFinder directory as the input for the pairs list. Choose any name of your choice for the output file name. 

Parameters Used in Test run

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 as the user defined it.

Tool Source for App

  • This is a standard perl-based parser for blast modified to allow for parsing based on various criteria.
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