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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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 ...
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1answer
168 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. ...
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22 views

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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20 views

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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181 views

RATT works on example bacterial sequence and other bacterial genome but not on C. elegans genome and annotation

I am trying to use a tool called RATT described in this paper and available here. I ran the example using the following command: ...
2
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0answers
49 views

What is tRNAscan-SE bit score?

I have used the command-line version of tRNAscan-SE by Lowe et al. (1997) on the reference genome sequence of C. elegans to predict tRNAs. The programme outputs a table with tRNA locations, amino acid,...
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16 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. ...
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24 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 ...
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21 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 ...
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0answers
119 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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59 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' ...
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16 views

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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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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28 views

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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22 views

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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16 views

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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16 views

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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111 views

Downloading full search results from BlastKOALA?

I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: https://www.kegg.jp/blastkoala/ When you get results, there are links for ...
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90 views

Detect gene duplication events from a whole genome in FASTA format

Are there any tools for finding duplications from a whole genome in FASTA format? Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the ...
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15 views

Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

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 ...
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9 views

How to interpret KEGG's qualifiers in gene list for Cyanidioschyzon merolae?

Looking at the gene descriptions of Cyanidioschyzon merolae's gene in the KEGG REST API, it is not clear to me what some of the qualifying adjectives mean. My understanding is that they have (mostly) ...
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72 views

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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30 views

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
41 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 ...
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1answer
92 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 ...