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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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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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
...
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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 ...
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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 ...
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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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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
...
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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. ...
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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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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:
...
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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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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 ...
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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):
...
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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 ...
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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 "...
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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.
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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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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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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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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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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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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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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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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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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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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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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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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 ...
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An error with annovar
I want to install annovar but in one particular part I always get this error
...
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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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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, ...
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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 ...
