Questions tagged [genome-annotation]

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How to train annotations tools

I would like to train Augustus, SNAP and GlimmerHMM. I found protein sequences in GenBank and orthodb.org. Furthermore, I found HMM files on busco-data.ezlab.org. ...
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22 views

Search for specific sequence in group of bacterial genomes

I have a group of L. plantarum genomes. I identified the pangenome using Roary. From the pangenome, I was able to identify unique 'genes' for some of the strains. One of these (actually several were, ...
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66 views

Genome annotation

I have helped a lab sequence a mitochondrial genome. I used then MITOS to annotate the genome (warning them that I did it just for curiosity as I am not experienced). They submitted the sequence and ...
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37 views

How to annotate optimally a fungal genome without RNA-seq evidence?

Genome information: ~50M nt 2300+ contigs No pre-trained parameters in Augustus There are several well annotated RefSeq genomes of this genus. There are several RNA-seq data of this genus, but not in ...
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200 views

How to fix "expired or not present file ~/.gm_key!" error in braker?

I'm trying to run a braker with genome file only to see if it's working or not before running with all the datasets. But I'm getting this error again and again. ...
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295 views

How to fix RepeatMasker.lib.nsq missing error when running RepeatModelor?

I have run RepeatModelor and I don't see the classified output file. I got this error. ...
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1answer
76 views

SNPEFF genome build with specific codon usage

Failing to build my own Arabidopsis thaliana reference with Mt using 'codon.Mitochondrial' and Pt using 'codon.Bacterial_and_Plant_Plastid' but the same commands works well with both lines with codon ...
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16 views

SwissProt Proteins into my Jbrowser

How is it possible to get the SwissProt Proteins into my Jbrowser in the same way like shown below? Thank you in advance,
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1answer
36 views

Why are my genes filtered for Gene Ontology term enrichment?

When I enter a list of gene names into common gene ontology (GO) term enricher (e.g. MsigDB or ToppGene) only a small fraction of genes is actually used for the enrichment: I am struggling to ...
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1answer
276 views

alternatives to PHASTER phage annotation server

I would like to use PHASTER (http://phaster.ca) from the University of Alberta, but it's currently down for maintenance, as is its predecessor, PHAST. What alternatives to PHASTER are there for ...
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53 views

Annotating conserved protein domains in bacterial assemblies

I understand the basic principles under which RPS-BLAST operates: search a protein (rpsblast) or nucleotide (rpstblastn) query ...
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75 views

Does Prokka do six-frame translations?

Does Prokka do six-frame genome annotations? The corresponding publication does not mention it. Seemann, Torsten. 2014. “Prokka: Rapid Prokaryotic Genome Annotation.” Bioinformatics 30 (14): 2068–...
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247 views

Gene function annotation - bacterial genome

I'm trying to annotate a genome to find all genes with a specific function. I have a FASTA and the read FASTQs - I'd like to assign the functional group of the identified proteins (e.g. Kegg orthology)...