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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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 ...
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Retrieve detailed gene descriptions
Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
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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 ...
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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 ...
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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" ...
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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 ...
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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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Obtain CD (cluster of differentiation) marker expression information
There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so ...
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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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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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