The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

Blat (default)

Blat (default) is the default form of Blat, the Blast-Like Alignment Tool.

Quick Start

Test Data

Input File(s)

Use the E. coli K12 genome from http://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=fasta&log$=seqview&format=text
and the homoserine kinase gene sequence from http://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=fasta&log$=seqview&format=text&from=2801&to=3733 as test data. Use Import from URL to get the data into your Discovery Environment account.

Parameters Used in App

There are no parameter settings for Blat (default). All settings are preset as default.

Output File(s)

Expect a tab delimited txt file as output, named output.psl. It is in psl format, which can be converted to SAM format.

Tool Source for App