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.

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3 votes
2 answers
48 views

Finding annotated counterpart after BLASTn with efetch (Biopython)

I am creating a pipeline for the identification of unknown transcripts. After a local BLASTn search of the transcripts, I have a large list of the respective hits with different genomes. I have the ...
1 vote
0 answers
114 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 ...
2 votes
0 answers
15 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 ...
2 votes
1 answer
42 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 ...
2 votes
1 answer
70 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 ...
6 votes
1 answer
142 views

Bacterial genome annotation of a clinical isolate strain?

So I'm basically so new to this that I'm just trying to find out what tools, methods, and keywords I should go look up by myself. I have a unique strain of a bacteria. I was given RNAseq data for ...
3 votes
1 answer
71 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 (...
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 ...
3 votes
1 answer
232 views

Get genomic coordinates using GenomicFeatures by HGNC gene names

I want to get coordinates of human genes from my list (consisting of hgnc genes id) using GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene R packages from Bioconductor. ...
3 votes
2 answers
72 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 ...
1 vote
2 answers
68 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 ...
2 votes
1 answer
55 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.
1 vote
1 answer
38 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 ...
3 votes
1 answer
239 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 ...
5 votes
1 answer
89 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 ...
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 ...
1 vote
0 answers
28 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 ...
1 vote
0 answers
17 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 ...
7 votes
1 answer
2k views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
1 vote
2 answers
108 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 ...
2 votes
0 answers
223 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 ...
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 ...
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 ...
3 votes
1 answer
201 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 ...
3 votes
3 answers
255 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 ...
4 votes
1 answer
321 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 ...
2 votes
1 answer
70 views

RNA seq fasta file annotation from alignment to reference matches

I've got a fasta file with some RNA seq data and another csv file with the output from plast where I've aligned it to a reference using plastn. I'm struggling with figuring out a command to append my ...
8 votes
1 answer
61 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 ...
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 ...
2 votes
0 answers
54 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. ...
1 vote
1 answer
52 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, ...
3 votes
3 answers
926 views

How can I find the chromosomal location of a list of genes?

I have a list of genes nearly 20000: gene name (column1) and coordinates (columns 2 and 3) ...
1 vote
0 answers
655 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 ...
3 votes
1 answer
38 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: ...
2 votes
2 answers
174 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 ...
1 vote
3 answers
89 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
91 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: ...
1 vote
0 answers
131 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): ...
1 vote
1 answer
345 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 ...
0 votes
1 answer
156 views

Given a .gb file and a locus - how to get relevant annotations in Python?

Given a .gb file and a specific locus in the genome - how can I parse the relevant annotations in Python (i.e., annotations that include that locus)? I import the ...
3 votes
0 answers
238 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 ...
1 vote
2 answers
94 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/...
1 vote
1 answer
124 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 ...
1 vote
0 answers
87 views

UTR features in gbk files

I have a gbk files for a viral genome that I have used biopython to add features of the 3' and 5' ...
3 votes
3 answers
2k views

Annotation with Prokka or RAST

I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank (NCBI Reference Sequence: NC_003389.1). I ran those sequences on Prokka and RAST ...
1 vote
0 answers
23 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 ...
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 ...
2 votes
2 answers
138 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 ...
4 votes
0 answers
34 views

Do RepeatModeler results contain functional domains?

The repeat families predicted by RepeatModeler contain known transposable elements (TEs) and unknown ones. How do we know whether some of these may actually: within a functional domain of a gene or ...
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 "...