Skip to main content

Questions tagged [sequence-annotation]

The process of attaching contextual information to a biomolecular (DNA, RNA, or protein) sequence, such as the location of genes, promoters, or repeats in genomic DNA, or the function of a protein.

Filter by
Sorted by
Tagged with
3 votes
1 answer
53 views

Unable to install prokka using homebrew or conda

I have tried to install prokka using homebrew using the code brew install prokka (I also tried brew install brewsci/bio/prokka) ...
Lucy Kelly's user avatar
1 vote
0 answers
25 views

How to compare CDS, CNE, miRNA, UCNE across new related genomes?

I have 5 sets of raw Illumina whole genome shotgun data from 5 different species, and 3 reference genomes that are assembled/annotated, I want to produce a similar table to Table S2 of this paper: ...
JohnDoe23's user avatar
1 vote
1 answer
23 views

Why is mtDNA not labelled as such for many organisms?

Also posted on biostars While I was searching the genomes of some eukariotic organisms (fungi,plants,protists) even though I knew that they had mitochondrial DNA,when I searched their genome structure ...
George X.'s user avatar
2 votes
0 answers
17 views

Confusing naming in MANE GFF file

I'm working with the MANE v1.2 annotation (with RefSeq keys) and am puzzled about the ID naming convention being used. Specifically, there are several transcripts (18 by my count) that have hyphenated ...
merv's user avatar
  • 651
2 votes
1 answer
44 views

Dog (Canis lupus familiaris) MT gene annotations

I have an RNA-Seq and scRNA-Seq dataset from dog samples and pseudo-aligned them to the dog reference transcriptome (Ensembl release 109). When filtering for mitochondrial gene percentage in scRNA-Seq ...
Alexandria Kouri's user avatar
3 votes
1 answer
80 views

How to annotate a bacterial genome automatically?

We recently got some shotgun sequencing results from a soil bacterium. And we have obtained some contigs which have some genes of interest. Is there a way to automatically annotate the whole sequence (...
Irfan's user avatar
  • 81
3 votes
2 answers
76 views

What is the best Query to retrieve DNA from NCBI?

I want to retrieve a sequence for many species from the Nucleotide database in NCBI. I'm using a command line approach and I have to figure out what is the best query that will return exclusively the ...
Mirko's user avatar
  • 267
1 vote
1 answer
30 views

Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?

I'm currently doing my thesis with the topic of phylogenetic analysis and is taking references from the previous person in my university (who have done the same topics but different species). They ...
Ayu Rani's user avatar
2 votes
1 answer
82 views

How to interpret a GenomeScope plot?

I am working on a new sponge genome and I have produced the genomescope plot from the 21-mer kmer frequencies. I have hard time interpreting the plot. Can someone please help me? Thank you.
Mudith Ekanayake's user avatar
1 vote
1 answer
53 views

Identifying the promoter on the reverse strand using visualization software (seqmonk)

I feel like this might be a really silly question and I've been going back and forth for awhile and I think confusing myself- so sorry if this is dumb. I am using Seqmonk to visualize genes in an ...
user18170's user avatar
0 votes
0 answers
18 views

The current status of human genome annotation

I was wondering if you can suggest something on the current status of the human genome annotation efforts. I know about ENSEMBL/HAVANA/GENCODE, and I've read the relevant papers; however, I was ...
Alexander Predeus's user avatar
1 vote
0 answers
29 views

David tool online not converting most genes

I'm using DAVID tool online, in order to perform functional annotation chart. I extracted the most relevant genes from a dataset (GSE73304), but have the problem that DAVID is not able to understand ...
Riesz98's user avatar
  • 41
5 votes
1 answer
91 views

Why is there gene without annotated location?

I came across this gene Pepc (peptidase C) NCBI gene database has a page for it here https://www.ncbi.nlm.nih.gov/gene/109616 But it does not contain any information on its coding sequence or genomic ...
geom_na's user avatar
  • 237
1 vote
2 answers
72 views

Extract data from genome

This question was also asked on Biostars 3 months ago, i.e. a long time - so its perfectly reasonable for the question to be asked here I started studying bioinformatics and I enjoy it a lot (I'm a ...
Sorin Trimbitas's user avatar
1 vote
0 answers
161 views

Prokka + table2asn (NCBI submission)

I have a couple of MAGs of interest that I am trying to submit to the NCBI (with annotations). The process of submitting the annotations is rather challenging to me. I have the output of Prokka, which ...
Laura's user avatar
  • 907
1 vote
0 answers
20 views

How Can You Reformat an OTU Table from qiime2 pathway to Include Sequence IDs?

I am trying to run Tax4Fun in MicrobiomeAnalyst, but am running into trouble with my table formatting. From the qiime2 pathway, I have an OTU, metadata and taxonomic table formatted like so: In ...
shannonevelyne's user avatar
2 votes
0 answers
251 views

PROKKA setupdb / cmpress error

I am trying to run --setupdb in Prokka, but I'm getting this error that I can't seem to find the answer for. When I run prokka --setupdb I get ...
Carol Luz's user avatar
0 votes
0 answers
42 views

What tool(s) can I use to use a .faa file to feed into JSMol?

JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
Harish Prabhakar's user avatar
3 votes
1 answer
63 views

Which human reference genome version does VARAdb use?

I am interested in annotating a list of variants using VARAdb. My coordinates use the GRCh38 (hg19) reference genome. However, I do not know which coordinate system VARAdb uses. A section of the ...
Cristian Riccio's user avatar
3 votes
1 answer
223 views

Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka

I am trying to run the Prokka annotation tool on my linux machine and have installed Barrnap and added it to $PATH and given the folder chmod 777 permission. However, when running Prokka, it gives the ...
Harish Prabhakar's user avatar
2 votes
1 answer
76 views

Sanger sequencing annotation error

I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
user avatar
0 votes
1 answer
27 views

I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?

I have a partially described gene from a plant with CDS and 3'UTR described but no 5'UTR; if I know the locus and upstream and downstream regions, is there a tool I can use for predicting regulatory ...
user16622's user avatar
2 votes
0 answers
55 views

In VEP annotation, how is the codon field interpreted?

After annotating with VEP a VCF file, we obtain different fields. One of them is called Codons which represents the affected codon in the transcript of the gene. ...
user324810's user avatar
  • 1,125
1 vote
1 answer
58 views

Why do Illumina 850k/EPIC arrays ignore CpGs which are "GC" in the forward strand?

CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC --- and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, ...
ning's user avatar
  • 141
1 vote
0 answers
809 views

conversion of a gbff file to a gff file

I want to get the annotations in gff format for a assembled genome. But for some species there is no available annotation in gff format in NCBI but only in gbff format. And I don’t know how to convert ...
Kishor Kumar Sarker's user avatar
3 votes
1 answer
39 views

What does it mean when a gene and its transcript have opposite orientations in a GFF3 file?

I was working with a given GFF3 file, and I observed that some transcripts have orientation opposite to their transcripts. Here is a snippet: ...
Maximilian Press's user avatar
2 votes
2 answers
201 views

Get genome coordinates from UniProt entry?

I'm trying to get genome coordinate information programmatically for multiple genes. As an example, I'd like to get the annotation (list of exons and their chromosomes, starts, and ends) for this ...
Michael Dunne's user avatar
1 vote
3 answers
91 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 ...
Gimme the 411's user avatar
1 vote
1 answer
96 views

Gencode PolyA feature annotation GTF gene_id not the same as Comprehensive gene annotation GTF

I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this: ...
justinian482's user avatar
3 votes
1 answer
277 views

Find a genomic coordinates for a protein aminoacid position

Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number. For example, I have KRAS gene for which I would like ...
lizaveta's user avatar
  • 203
1 vote
0 answers
138 views

snpEff annotation and variant in a gene

I'm using snpEff to annotate genetic variants. However, the annotation often returns more than one annotation (see below for an example): ...
Anti's user avatar
  • 153
1 vote
1 answer
374 views

Different line length in fasta file

I am currently using VEP for variant annotation. I am facing an error as below: [E::fai_build_core] Different line length in sequence 'Pn9' I understand there is ...
Sowmya Pulapet's user avatar
3 votes
0 answers
259 views

How to remove redundancy from a gtf file?

I have an annotation file. I would like to remove redundancy, as shown in the example (in the real file, I have a lot of these redundant cases). I would like to consider only one of the following ...
Marco's user avatar
  • 161
1 vote
2 answers
96 views

How can I get latest .vcf files with annotation data?

I'd like to perform the annotation (1000genomes, COSMIC etc.) of my variants using SnpSift and SnpEff, however so far all I get are vcf files for separate chromosomes: http://ftp.1000genomes.ebi.ac.uk/...
Adamm's user avatar
  • 206
4 votes
1 answer
365 views

On the same strand, for the same gene, can exons be overlapping?

I want to get a set of exon regions for each protein coding gene. I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
gc5's user avatar
  • 1,813
1 vote
1 answer
139 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 ...
raysteven's user avatar
1 vote
0 answers
25 views

Why does gene count increase drastically after scaffolding with Hi-C data?

I have a conceptual question. I have a diploid, outcrossing plant genome assembly of ~1.1 Gb size. The original assembly is generated from PacBio reads. After genome annotation with the ...
Anik Dutta's user avatar
2 votes
2 answers
150 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 ...
mrPuzzle's user avatar
1 vote
0 answers
23 views

How to get a list of all human morphogens?

Gene Ontology provides many genes annotated as taking part in various morphogenesis processes but I want to get a list of all morphogen coding genes specifically. Uniprot does not have "...
Sashko Lykhenko's user avatar
0 votes
0 answers
93 views

An error with annovar

I want to install annovar but in one particular part I always get this error ...
Zizogolu's user avatar
  • 2,160
3 votes
3 answers
274 views

Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)

Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these? For the moment I ...
aechchiki's user avatar
  • 2,676
1 vote
1 answer
61 views

replacing periods with hyphen

I am a software engineer and not a bioinformatician. I am looking at some code where they are looking at aligned proteins that are in the A2M alignment format (https://compbio.soe.ucsc.edu/a2m-desc....
Luca's user avatar
  • 113
0 votes
1 answer
358 views

What does 'Human Alternative sequence Gene' mean in Ensembl?

I have downloaded a dataset containing RNA-Seq RPKM (reads per kilobase per million) values for 52376 genes (in humans). To find RPKM values for the gene KIR2DL2 in the dataset, I have to search for ...
ceno980's user avatar
  • 159
3 votes
3 answers
201 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/...
raysteven's user avatar
1 vote
1 answer
333 views

Ensembl Variant Effect Predictor (VEP) issue during execution

I got this error during execution, pls guide me. ...
sakshiR's user avatar
  • 11
1 vote
0 answers
33 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. ...
user3523406's user avatar
2 votes
1 answer
58 views

Demovir produces an empty output

I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs. First, I installed all ...
Ernie Hsieh's user avatar
2 votes
1 answer
384 views

Transfer annotations from one genome assembly to another

I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length ...
hac's user avatar
  • 21
1 vote
2 answers
110 views

Problem with Seurat reference mapping

I have 10X scRNA-seq multiome's 3' poly-A capture (scRNA-seq+ATAC-seq) from PBMC Using Seuratreference mapping, I mapped my scRNA-seq part on reference PBMC (for ...
Zizogolu's user avatar
  • 2,160
2 votes
1 answer
86 views

Splice variant analysis with ensembl genome/annotation/rna. Which files do I use?

I am running splice variant analysis. I wanted to use NCBI genome but the program works better with ensembl. I am a bit confused on primary vs. top level to use as my reference genome. I also do not ...
Christa Frodella's user avatar