Questions tagged [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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25 views

Why is there a discrepancy between the number of markers on panglaodb.se and on the downloadable .tsv file for all markers? [closed]

I've noticed that there were only about ten markers shown for pericytes in the .tsv file while the table on the website showed over 50. What is the cause of this discrepancy?
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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 ...
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28 views

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 ...
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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 ...
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1answer
42 views

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
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Do RepeatModeler results contain functional domains?

The repeat families predicted by RepeatModeler contain known TEs and unknown ones. How do we know whether some of these may actually be a functional domain of a gene? It's predicted as repeats may ...
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1answer
52 views

How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...
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53 views

Prokka error message

I am trying to run Prokka but the following error message appears: Could not run command: makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.7-gompi-2019a/db/kingdom/Archaea/sprot ...
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How to annotate ChIP peaks base on NCBI sequence name?

I have chip-seq peaks based on NCBI genome which looks like the following: ...
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1answer
112 views

annotation using ChIPseeker package error

I have differential binding sites object obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, ...
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143 views

How to fix “expired or not present file ~/.gm_key!” error in braker?

I'm trying to run a braker with genome file only to see if it's working or not before running with all the datasets. But I'm getting this error again and again. ...
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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' ...
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Finding the relevant annotations for biomarkers

I am looking to find a way to map a list of biomarkers of interest, say genes or bacterial functions, to existing annotation databases. Usually this is done in reverse, as such that based on ...
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Finding original papers for gene annotations

I am wondering if there's a database to look up the annotation history of an arbitrary gene/ORF, with links to the primary literature for each step of the annotation. I have found that neither NCBI ...
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34 views

Inheritance annotation for nsSNPs

I am relatively new to SNP analysis. Is there a database to find annotation about the Mendelian inheritance of SNPs? I have a small list of nsSNPs (non-synonymous SNPs) and I need to find how they are ...
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31 views

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results with TransDecoder....
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990 views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...
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707 views

How to add cluster name to metadata in Seurat?

I'm working on a Seurat object and want to name the clusters according to 2 values alone (yes/no). So I want to add a new column to metadata and annotate the clusters (UMAP) with it. ...
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1answer
107 views

Decontaminating RNA seqs for de novo transcriptome assembly and annotation of novel eukaryotes

I have raw paired-end RNA-seq reads for two novel eukaryotic species. Some background: the reads represent a copepod (arthropod) species each. The mRNA for each read set was obtained by extracting ...
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differential analysis of chip-seq data

I have several sets of chip-seq data. I called the peaks using Macs2. I am pretty new to the field and I will appreciate any help. I wanted to annotate the peaks and see which peaks are shared between ...
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How does one go about developing GCMS metabolite annotation workflow?

I’m really new to untargeted metabolomics and I need to annotate a data set from a standard quadrupole GCMS. The person on the project before me tried to do the annotation manually, cleaning up the ...
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Gffcompare issue: 0 reference transcripts loaded

I am trying to use gffcompare to compare my assembled transcriptome to a reference gtf that contains information about small open reading frames (sORFs). The reference gtf was obtained by processing ...
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Determining a Gene's Unknown Function

I'm a beginner in this field (so pardon my rudimentary knowledge/explanation) trying to understand ways on how I could potentially identify genes of unknown function. I am trying to get as close as I ...
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1answer
526 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 ...
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How to (efficiently) search nuccore to retrieve only annotated sequences?

I wish to efficiently search nuccore to retrieve only annotated sequences. By "annotated" I mean that the nuccore entry contains annotation information. An equivalent definition (if I understand ...
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Is there a built-in parser for the textual feature table that Entrez.efetch returns?

Entrez.efetch helpfully gives me the feature table of a nuccore entry. If I understand correctly, efetch can only return the ...
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1answer
79 views

Filtering VEP annotation file

I am filtering a VEP annotated vcf, trying to maintain just those variants classified as deleterious by SIFTand as damaging (probably or possibly included) by ...
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121 views

Getting sequences of one transcript per gene out of annotation and genome

I got a genome (data/genome/genome.fasta) and braker-based genome annotation (data/genome/annotation.gff3), now I would like to ...
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1answer
52 views

REMC SNP annotations for transcriptome prediction - epiXcan

I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper: https://www....
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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,
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2answers
188 views

RepeatMasker annotation

I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and ...
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1answer
131 views

Ensembl protein identifiers from different assemblies

In order to obtain orthologs for human genes, I am working with InParanoid version 7.0. This version of the database uses Ensembl Protein Identifiers (ENSP) from ENSEMBL version v54, which is based on ...
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1answer
103 views

renaming IDs in gff3 with BCBio.GFF

I wrote a script which should changes IDs in a GFF3 file. Unfortunately, the below script has two problems. It attaches the new ID to Parent which leads that ...
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1answer
67 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 retrieve the relevant annotations in Python (i.e., annotations that include that locus)? I could ...
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1answer
59 views

where to find pathogenicity metadata for E.coli genomes

I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.: ...
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3answers
285 views

Modifing a GFF3 file and writting to a new file

I modified the GFF3 file with the below code: ...
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1answer
62 views

Adding an attribute to GFF3 file

I failed to add Note=Gene description to mRNA attribute with the below code: ...
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1answer
57 views

Are there databases to annotate non-coding mutations?

I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome? Preferably, if the database is downloadable so I am able to ...
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4answers
122 views

Merging two .txt files

I have two .txt files and let's call it 'File A' and 'File B.Here are examples of what file A and file B looks like: FILE A ...
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2answers
393 views

How to retrieve the subcellular location info from uniprot?

I have a list of proteins with their gene names/symbols. I would like to identify which of them are extracellular proteins or plasma membrane proteins. I can get this information in UniprotKB by ...
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1answer
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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 ...
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1answer
12 views

SnpEff gene annotation with @ such as PCDHB@

I'm using snpEff to annotate some VCFs and getting some spurious annotations that don't have transcript ids. Some of these annotations have a gene name followed by ampersand such as PCDHB@ and I'm not ...
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1answer
85 views

ANNOVAR, 1000g database calling

I have recently downloaded Annovar, and succesfully filtered my files with a few databases, downloaded from Annovar. But when I try to do the exact same thing with the 1000 genomes project database, I ...
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1answer
113 views

What is the `table` parameter in the UCSU ldHgGene tool?

I want to lift over the annotation from E. coli release 29 to E. coli release 42. I have followed the steps for an annotation liftover mentioned here. I got the chain file for the final step and ran: ...
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1answer
48 views

No refseq transcripts in 2nd half of Y chromosome for HG38

Obviously there is a gap in my understanding of how sex chromosomes are annotated. I've been working on some CNV calls and noticed that most of the 2nd half of ChrY is missing annotations and no reads ...
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Evidence of emergence of “genuine” novel protein interactions by aa mutation [closed]

Anyone knows of an example of a protein that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other ...
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1answer
77 views

Genome annotation of a Bacillus strain

I finished the sequencing of the genome of a biocontrol activity strain Bacillus amyloliquefaciens by Illumina hiseq. I have already gone through some papers but there were no details of processing in ...
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1answer
204 views

A GTF annotation for GRCH375d version

I have been given a bunch of .bam files, that come from the alignment on GRCh37d5 of human genome by Star tool. I want to extract raw read counts from these bam files by FEATURECOUNTS tool so I need a ...
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The best tool to count the number of insertion sequences in a set of bacterial genome

I have a set of 414 GenBank genomes and I need to count a number of insertion sequences (ISs, transposases) in each of them. Is there any traditional way to perform such an analysis? I came up with ...
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1answer
357 views

Why doesn't the mouse GRCm38/mm10 refGene genome annotation file contain non-coding transcripts?

I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species. My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the ...