Questions tagged [genome-annotation]
The genome-annotation tag has no usage guidance.
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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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1answer
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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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,
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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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1answer
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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1answer
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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2answers
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)...
