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-112913

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Korf lab's gene-finder.

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

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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 -> snap_gene_prediction.

Input File(s)

  1. Fasta file: Use arabtest2.fa from the directory above as test input
  2. Hmm file: Use  A.thaliana.hmm for the HMM file.

The other HMM 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

Options

Plus strand - To predict on plus strand only

Minus strand - To predict on minus strand only

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You should only select either of plus or minus strand options but not both


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 test.aa, test.fa and test.gff

Tool Source for App

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