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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Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

What are the actual differences between different annotation databases? My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation)...
Plasma's user avatar
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19 votes
6 answers
3k views

Are there any RepBase alternatives for genome-wide repeat element annotations?

I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements. This works well enough, and seems to be the de ...
Konrad Rudolph's user avatar
12 votes
1 answer
527 views

How to calculate overlapping genes between two genome annotation versions

I have two annotations of the same genome generated with different annotation pipelines. I want to identify overlapping gene models. An important feature of this genome is that there are many 'genes ...
holmrenser's user avatar
10 votes
3 answers
1k views

Tools to create annotated table of variants from VCF

The problem: I have a VCF file, a reference genome, and a bunch of annotations for the reference (genes, repeat regions, etc.) as GFF or BED files. What I would like is a tool that takes all of this ...
roblanf's user avatar
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10 votes
4 answers
274 views

Annotation format design

Bashing file formats is a favorite pastime in bioinformatics, and annotation file formats such as GFF and BED seem to get special attention. A lot of this frustration stems from community's shockingly ...
Daniel Standage's user avatar
9 votes
2 answers
2k views

5'UTR and 3'UTR annotation in yeast

I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of Saccharomyces cerevisiae yeast genes. The problem is finding a ...
plat's user avatar
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9 votes
2 answers
506 views

How to transfer gff annotations in genome with extensive duplications?

Microbial genomes can contain extensive duplications. Often we'd like to transfer annotations from an annotated species to one that is newly sequenced. Existing tools (e.g. RATT, LiftOver, Kraken) ...
scalefreegan's user avatar
8 votes
1 answer
1k views

How GFF3 attributes (9th column) varies from one gene prediction algorithm to another

GFF3 files are in tabular format with 9 fields per line, separated by tabs. The first 8 fields share almost same data structure, but the 9th field varies a lot depending on feature type and gene ...
Arijit Panda's user avatar
8 votes
2 answers
429 views

Comparing two genome annotations

I have one-dimentional array (human genome). Also I have two annotations for it, we can think about them as different peaks (it's nucleosome and secondary structures). How can we find correlation and/...
D M's user avatar
  • 181
8 votes
1 answer
62 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 ...
Alex Stuckel's user avatar
7 votes
3 answers
5k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
Peter's user avatar
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7 votes
3 answers
3k views

How to perform functional analysis on a gene list in R?

From an RNA-seq experiment I have about 17000 gene ids for 2 sample conditions arranged according to their log2 fold changes when compared to a control. I need to annotate these, but I've never done ...
J0HN_TIT0R's user avatar
7 votes
1 answer
1k views

How can I create my own GO association file (gaf)?

This question is based on a question on BioStars posted >2 years ago by user jack. It describes a very frequent problem of generating GO annotations for non-model organisms. While it is based on ...
Michael's user avatar
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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 ...
Reilstein's user avatar
  • 367
6 votes
2 answers
571 views

Same transcript coordinates in gtf file, different transcript ID

I have a gtf file from Ensembl, and I noticed that several "transcript" annotations have the exact same coordinates. See for instance the third and fourth transcripts ("Y74C9A.2b.1" and "Y74C9A.2b.4") ...
bli's user avatar
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6 votes
3 answers
799 views

Identify non-coding regions from a genome annotation

I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome: ...
Zizogolu's user avatar
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6 votes
1 answer
144 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 ...
myflow's user avatar
  • 63
6 votes
2 answers
1k views

Transcript Coordinate Ranges to Genomic Coordinates

I have 2 GFF3 files: Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space. Features using chromosome IDs as the landmarks. i.e. "exon" ...
Nathan S. Watson-Haigh's user avatar
6 votes
0 answers
65 views

Why does repeatmasker annotate transposons of length 1?

I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from ...
Biomagician's user avatar
  • 2,459
5 votes
4 answers
2k views

tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable

I have downloaded tRNAscan-SE from here. After decompressing and untaring the file, I installed it using: ./configure make make install When I type ...
Biomagician's user avatar
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5 votes
5 answers
221 views

Where is an up to date miRNA database and what happened to miRBase?

miRBase 21 was published June 26, 2014 and was still in its growth phase. Why is it not being updated anymore or the project declared officially dead? ENSEMBL also uses miRBase as a starting point (...
Ido Tamir's user avatar
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5 votes
1 answer
89 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–...
Soerendip's user avatar
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5 votes
2 answers
1k views

Difference between de novo transcriptome assembly methods

I have been looking around (including read the original papers) to understand what is essentially the difference between StringTie in non-reference based mode (de novo) and Trinity de novo assembly. I ...
kaka01's user avatar
  • 111
5 votes
2 answers
259 views

Software recommendation: find DNA sequence distribution over entire transcript

I would like to create a density/histogram of the distribution of a particular DNA sequence over the entire transcript using R and/or command line tools. From here, I would like to use the coordinates ...
syntonicC's user avatar
  • 161
5 votes
1 answer
4k views

hg38 GTF file with RefSeq annotations

I'm not sure what I'm missing, but I'm struggling to find an official hg38 GTF file with RefSeq annotations. I'd like to provide ...
Mark Ebbert's user avatar
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5 votes
1 answer
1k views

Derive a GTF containing protein coding genes from a GTF file with Exons and CDS

Why I need a compatible file I’m trying to run velocyto with the R package to analyse RNA velocity (cell trajectories) with single cell RNASeq data. I have performed single cell analysis from 10x ...
Tom Kelly's user avatar
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5 votes
1 answer
408 views

Keep Format and Individual fields when annotating VCF with VEP

I'm currently updating my Variant Calling Pipeline by switching the VCF annotating software from Annovar to VEP for a variety of regions, not least how easy it is to annotate with HGVS notation and ...
JSneathThompson's user avatar
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
4 votes
4 answers
127 views

In GFF3, annotating more than one protein-coding gene (i.e. polycistronic) contained in a eukaryotic mRNA

Below is an example of a simple GFF3 file: ...
l0110's user avatar
  • 292
4 votes
2 answers
115 views

How can I use annotations to remove variants not relevant to cancer risk?

I currently have ~180 whole germlines and around 10M SNPs/indels. I would like to build a predictive model using Machine Learning (ML) techniques to predict cancer risk according to these germline ...
Ezequiel's user avatar
4 votes
1 answer
345 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
  • 1,783
4 votes
2 answers
337 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)...
MichaelKirst's user avatar
4 votes
1 answer
2k views

What does the number mean in an HGVSp annotation?

Let's take the example p.Arg452Pro that I got from an annotated VCF file that contains an HGVSp column. What does ...
user324810's user avatar
  • 1,115
4 votes
1 answer
49 views

In SBOL, when should I annotate a DNA sequence vs. making sub-components?

When representing a DNA sequence in SBOL as a ComponentDefinition, you can mark things like promoters and coding sequences in two different ways: either as a ...
jakebeal's user avatar
  • 653
4 votes
1 answer
2k views

COG Annotation - Dealing with genes assigned to two or more COG categories

I am dealing with a list of genes which have been selected from a gene enrichment analysis. In order to see what kind of genes are overrepresented, I ran eggnog-mapper to do an orthology assignment of ...
Sergio Arredondo's user avatar
4 votes
1 answer
246 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
  • 1,679
4 votes
2 answers
165 views

How to predict stop codons in Illumina reads?

I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a ...
francoiskroll's user avatar
4 votes
1 answer
1k views

get gene lines from gtf file

I would like to retrieve gene lines from a GTF file for which I only have exons & transcripts lines (output from Cufflinks) and alternative splicing possible. I need gene lines for compatibility ...
aechchiki's user avatar
  • 2,676
4 votes
0 answers
36 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 ...
Life_Searching_Steps's user avatar
3 votes
5 answers
253 views

Import a tab-separated file with differing numbers of elements in each row; prokka output

I am using prokka to annotate a bacterial genome: prokka ecoli.fa Prokka is outputting a tab-separated file (called PROKKA_12142017.tsv) with differing numbers of ...
Biomagician's user avatar
  • 2,459
3 votes
4 answers
748 views

Basic questions about GSEA

I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, ...
J0HN_TIT0R's user avatar
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
3 votes
4 answers
274 views

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

I downloaded the annotation of the C. elegans genome in GFF3 format from Ensembl. I typed the following command, hoping to get the header of the file (lines starting with ...
Biomagician's user avatar
  • 2,459
3 votes
3 answers
948 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) ...
Anna1364's user avatar
  • 516
3 votes
1 answer
204 views

Why do BLASTn and prokka not seem to be searching the whole fasta file?

When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome. Starting with a ....
Daniel Harris's user avatar
3 votes
1 answer
78 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
73 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
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
216 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
3 votes
3 answers
265 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