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36 (with



Blat_with_options is an app for Blat, the Blast-Like Alignment Tool. This version allows setting options.

Quick Start

Test Data


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

Input File(s)

Use the E. coli K12 genome from$=seqview&format=text
and the homoserine kinase gene sequence from$=seqview&format=text&from=2801&to=3733 as test data. Use Import from URL to get the data into your Discovery Environment account.

Arabidopsis_thaliana.TAIR10.fa as the database file and

AT3G24310.fa as the query file

Parameters Used in App

There following settings can be used:


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

Tool Source for App