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Questions tagged [gene-annotation]

Gene annotation refers to the characterization of a gene's exon-intron-UTR structure.

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Where do I get an annotation file for yeast genome with ENSEMBL ids?

Even the annotation files hosted on the Ensembl site have systematic names (starting with Y..) instead of ENSEMBL ids (starting with EN..). I bet there would be a place where I can get an annotation ...
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How to categorize non-coding sequences in the genome?

I'm trying to wrap my head around the diversity of functions in a genome. Obviously, you've got coding and non-coding regions. But within "non-coding" regions, it seems to be a "wild west" to me. ...
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Reason for name “Motile sperm domain-containing protein 2” if it has nothing to do with sperm

I am interested in a gene with the name "motile sperm domain-containing protein 2". The entry for the human gene in uniprot suggests that it does not have any relation to sperm or spermatogenesis. ...
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Get protein annotation from Uniprot out of protein mappings

Having a file of for about 10k mapping identifiers how can I get the annotations of the proteins from Uniprot ? As it is not possible to do It manually My mappings are contained in a .csv file They ...
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Use of pipe character in VCF info field

While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance): ...
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Blastx: from gi to description

I have done a blastx and use the outfmt 6 option, because I want to work in the tables format. When I do this I get subject ids of the type sp|Q7XJS0|ASHR1_ARATH, sp|Q39547|CUCM1_CUCME, et cetera....
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How to annotate the SwitchGear gene models?

According to this page(http://switchgeargenomics.com/wp-content/uploads/2009/02/switchdb_technote1.pdf), the SwitchGear gene models can be annotated by the NCBI annotation associated with Refseq ...
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How valid are GO (Gene Ontology) terms?

I'm looking for papers quantifying the validity of ontologies such as GO. I'm relatively new to using annotation terms, and I often hear things like "annotation is messy" and "GO is good but it's ...
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Is there a free software for manual sequence annotation?

I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence ...
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How many genes does D. melanogaster have?

Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, ...
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How to annotate a .broadpeak file with 9 columns?

I have this peak file I retrieved from an ENCODE chip-seq matrix. Its .broadpeak file looks like this: ...
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No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package

I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: introduction to Chip Seq . The same as autor of mentioned question I am a student of Applied Mathematics and I ...
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In this illustration about CRISPR function, what do these objects mean (image provided)?

In the paper on CRISPRs, the following figure is shown: I added the light-green boxes. What do the red arrows and the line with a filled circle on the far left mean? What does the arrow in the ...
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What is the convention for indicating genomic primer sites?

What is the most common notation for indicating genomic binding sites of primers relative to an ORF? For instance, if I want to indicate a primer like so: ...
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How Scientists sequence, assemble and annotate plant genomes? [closed]

I previously read this question and this paper and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and ...
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Drosophila biarmipes gene annotation, transposable element?

When doing an annotation of a contig31 of Drosophila biarmipes genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in ...
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RNA-Polymerase III transcribed genes

I have a list of differentially regulated genes from a high-throughput experiment of the human genome. I would like to find out which of these genes are transcribed by a RNA polymerase III and which ...
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Is there a rule for the annotation of the basepair or gene locus origin in bacterial genomes?

Since all bacteria have one circular chromosome, there is no designated origin to start the systematic gene locus numbering. Therefore, what is the rule to start the numbering at a particular point (i....
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Understanding these SNP annotations

I am looking at the PharmaPGKB database for SNPs and trying to understand what the following annotation means: rs1801131 at 1:11854475 in CLCN6, MTHFR (VIP) Ok, ...
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Combining gene expression data from two species

I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
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Question: Annotation search in scientific literature

In a scientific paper I have been studying ("Predicting Novel Human Gene Ontology Annotations Using Semantic Analys" S.Draghici et al., 2010), I have read that authors checked the accuracy of their ...
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Overlapping genetic information in eukaryotes

In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do ...
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What are the limiting factors for gene length and number of exons?

I recently downloaded gene annotations for Homo sapiens from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have ...