Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Augustus gene prediction CDS problem joxcargator73 Bioinformatics 4 03-26-2015 04:58 PM
Best tool for gene prediction ? patouch74 Bioinformatics 4 08-10-2014 12:17 AM
[Gene Prediction] AUGUSTUS program syintel87 Bioinformatics 1 02-16-2014 09:15 AM
augustus gene finder condomitti Bioinformatics 2 11-23-2013 06:24 AM
survery: what assembler, gene prediction and gene annotation softwares do you use? Gorbenzer Metagenomics 6 04-22-2013 02:25 AM

Thread Tools
Old 11-07-2016, 09:31 AM   #1
Junior Member
Location: Connecticut

Join Date: Nov 2016
Posts: 1
Smile Gene Prediction: AUGUSTUS

Hello All,

I have sequenced and assembled the chloroplast genome of a red alga. I would like to use AUGUSTUS for gene prediction within my genome; however, I would like to choose an organism model as close to my species as possible. Does anyone know if there's a way to specify an organism model that's not already listed in AUGUSTUS? The model organisms I would like to use have fully assembled and annotated genomes.


- Amanda G
Amanda_G is offline   Reply With Quote
Old 11-08-2016, 04:34 AM   #2
Senior Member
Location: Germany

Join Date: Apr 2012
Posts: 215

If it is not yet available in AUGUSTUS, you may submit a new training request online:
WhatsOEver is offline   Reply With Quote
Old 11-23-2016, 11:22 AM   #3
Junior Member
Location: Brazil, SP

Join Date: Nov 2016
Posts: 1

I'm trying to train and predict UTR in transcriptome using Augustus.
I'm following the script (in augustus.2.5.5 version).

My command line:
sudo AUGUSTUS_CONFIG_PATH=home/augustus.2.5.5/config perl
/home/augustus.2.5.5/scripts/ --species=myspecie
--genome=genome.fa --trainingset=merged_annotations.gff --cdna=transc.fasta
-v --noninteractive --workingdir=/home/jordana/teste25 > GFF_step1

But, in first step (-- Construct an initial training set of genes (protein
coding regions thereof), e.g. using PASA) there are a something that stoped
the script. And every attempt the log (GFF_step1 file) returns and stop in
this part "2 First try with etraining: etraining --species=myspecie >train.out ...". Furthermore, below command line appear
just "failed to execute:".

I also tried use another data set (e.g. human genome and genbank human
genome), but I had the same problem. And I not have ideia what happens.
jordana is offline   Reply With Quote
Old 01-02-2017, 01:53 AM   #4
Junior Member
Location: INDIA

Join Date: Mar 2013
Posts: 2


I want to predict gene in buffalo dataset, which training dataset should I use? Do I need to train cattle data or human training dataset will work?

Anand Patel
AB.PATEL is offline   Reply With Quote

annotation, augustus, gene prediction, model organism

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:45 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO