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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Snap, gene prediction

Snap, gene prediction uses splicing information from different species to find transcript and coding sequences within a genome assembly. Snap takes a fasta DNA sequence file and produces a protein sequence file and a transcript sequence file, both in fasta format.

Quick Start

Test Data

Icon

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

Input File(s)

Use arabtest2.fa from the directory above as test input, and select, for example, A.thaliana.hmm.

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.

Use default names, and choose A.thaliana.hmm for the HMM file.

The other files available are:

Acanium.hmm
A.gambiae.hmm
A.mellifera.hmm
At.hmm
A.thaliana.hmm
B.malayi.hmm
B.mori.hmm
brugia
C.elegans.hmm
Ce.hmm
C.intestinalis.hmm
ciona
D.melanogaster.hmm
Dm.hmm
fly
ixodesA.hmm
ixodesB.hmm
mam39-ro.hmm
mam39.hmm
mam46-ro.hmm
mam46.hmm
mam54-ro.hmm
mam54.hmm
minimal.hmm
mosquito
Nasonia.hmm
nGASP.hmm
nGASPr.hmm
O.sativa.hmm
Os.hmm
rice
thale
worm

.

Output File(s)

Expect text files named after the input value for 'header' as output. For the test case, the output files you will find in the example_data directory are named proteins.fa and transcripts.fa.

Tool Source for App