Questions tagged [genome-annotation]

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1 vote
3 answers
62 views

How can I assemble my genome from raw files?

I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF). How can I assemble it? And does assembly provide any further ...
1 vote
1 answer
55 views

BPGA error: there was no protein data in file

I'm trying to do pan-genome analysis using BPGA and I face this error: This error didn't show up in the other data set where all the .gbk is downloaded from NCBI. This .gbk file is our own data and ...
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2 votes
2 answers
52 views

Find the genomic locations of exons of certain human gene

So I know Consensus CDS has the genomic locations of exons, however, only of the exons in the CDS. Everything before or after is not included. NIH variation viewer has those (kinda-) radio buttons ...
3 votes
3 answers
141 views

Does anyone know what tools are used to construct this beautiful genome map?

Does anyone know what tools are used to construct this beautiful genome map? The research paper didn't mention how to construct this map. Link to paper: https://www.sciencedirect.com/science/article/...
  • 121
1 vote
0 answers
25 views

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. ...
0 votes
0 answers
27 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, ...
  • 43
0 votes
2 answers
87 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 ...
1 vote
1 answer
59 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 ...
  • 81
1 vote
1 answer
499 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. ...
2 votes
1 answer
196 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 ...
  • 141
1 vote
0 answers
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 votes
1 answer
39 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 ...
  • 67
1 vote
1 answer
332 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 ...
  • 2,234
1 vote
1 answer
56 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 ...
5 votes
1 answer
78 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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7 votes
0 answers
35 views

dog coordinates (canFam3) to human coordinates (hg19)

I've converted dog coordinates to human using UCSC LiftOver*. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...
4 votes
2 answers
280 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)...