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

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252 views

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 ...
8
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3answers
149 views

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 ...
6
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1answer
78 views

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 ...
4
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2answers
102 views

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 ...
3
votes
1answer
101 views

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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1answer
62 views

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 ...
1
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1answer
22 views

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 ...
1
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0answers
46 views

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 ...
1
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1answer
86 views

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 ...
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7 views

Why low variant frequency in exomeseq data (ANNOVAR)?

I've got an annotated ANNOVAR file with 300.000 nucleotide variants of 4 genomes. There's one thing I don't understand when looking at the data: Why are the variant frequencies so low in comparison to ...