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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
165 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
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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 ...
sana amir's user avatar
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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
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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
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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
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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
36 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
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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
87 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
86 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
202 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
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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
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1 vote
1 answer
308 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
223 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
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2 answers
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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
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4 votes
1 answer
268 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
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1 vote
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115 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
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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
121 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
21 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
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0 answers
84 views

An error with annovar

I want to install annovar but in one particular part I always get this error ...
Angel's user avatar
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3 votes
3 answers
243 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
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1 vote
1 answer
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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
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1 answer
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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
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3 votes
3 answers
181 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
284 views

Ensembl Variant Effect Predictor (VEP) issue during execution

I got this error during execution, pls guide me. ...
sakshiR's user avatar
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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. ...
user3523406's user avatar
2 votes
1 answer
55 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
285 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
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1 vote
2 answers
104 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 ...
Angel's user avatar
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2 votes
1 answer
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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
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0 answers
32 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, ...
Mark's user avatar
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0 votes
2 answers
128 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 ...
juanjo75es's user avatar
2 votes
1 answer
71 views

Hg38 annotation tracks retrieval

I want to retrieve an annotation object (as GRanges) containing different UCSC annotation tracks such as CpG Islands, TSS, TFBS and promoters for hg38 Human reference genome. But "UCSC Genes"...
TRakesh's user avatar
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4 votes
1 answer
216 views

Annotating a .vcf with centimorgan information

Some programs (e.g. shapeit4) automatically annotate an INFO tag into a .vcf file which gives the cumulative genetic distance in cM between each SNP: ...
user438383's user avatar
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1 vote
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118 views

SnpEff not correctly annotating multiple-nucleotide polymorphisms

I have some SARS-CoV-2 sequencing data that I'm trying to annotate with SnpEff, however SnpEff doesn't appear to be recognizing multiple adjacent SNPs within the same codon and correctly calling them ...
Set's user avatar
  • 241
0 votes
1 answer
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Annotating gene names or gene IDs to a dataframe containing SNPs?

I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
Najeha Mohamed's user avatar