Questions tagged [genome-annotation]

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1answer
28 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 ...
0
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0answers
122 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. ...
1
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1answer
112 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. ...
0
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0answers
32 views

Why I get Singularity error when I try to run MAKER Genome Annotation on HPC?

I need to run MAKER genome annotation for my assembly file on HPC and I'm new to this. When I try to do that I get this error. ...
0
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0answers
15 views

Select for a specific proportion of a genomic feature

Currently have a bed file with exon coordinates for a list of about 20 genes, and I want to select the exons that fall within the first 3/4 or 2/3 of the coding region for each gene. Does anyone know ...
2
votes
1answer
36 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 ...
1
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0answers
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,
0
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1answer
33 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 ...
1
vote
1answer
240 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 ...
2
votes
1answer
47 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 ...
6
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1answer
74 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–...
5
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2answers
219 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)...