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.

24 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
3
votes
0answers
40 views

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 ...
3
votes
0answers
156 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. ...
2
votes
0answers
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 ...
2
votes
1answer
283 views

Why doesn't the mouse GRCm38/mm10 refGene genome annotation file contain non-coding transcripts?

I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species. My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the ...
2
votes
0answers
167 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
votes
0answers
39 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,...
1
vote
0answers
42 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' ...
1
vote
0answers
14 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 ...
1
vote
0answers
28 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....
1
vote
0answers
18 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 ...
1
vote
0answers
19 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 ...
1
vote
1answer
34 views

REMC SNP annotations for transcriptome prediction - epiXcan

I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper: https://www....
1
vote
0answers
15 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,
1
vote
0answers
14 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 ...
1
vote
0answers
94 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 ...
1
vote
0answers
84 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 ...
0
votes
2answers
36 views

differential analysis of chip-seq data

I have several sets of chip-seq data. I called the peaks using Macs2. I am pretty new to the field and I will appreciate any help. I wanted to annotate the peaks and see which peaks are shared between ...
0
votes
0answers
6 views

How does one go about developing GCMS metabolite annotation workflow?

I’m really new to untargeted metabolomics and I need to annotate a data set from a standard quadrupole GCMS. The person on the project before me tried to do the annotation manually, cleaning up the ...
0
votes
0answers
35 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 ...
0
votes
0answers
19 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 ...
0
votes
1answer
32 views

Filtering VEP annotation file

I am filtering a VEP annotated vcf, trying to maintain just those variants classified as deleterious by SIFTand as damaging (probably or possibly included) by ...
0
votes
0answers
12 views

miRNA Homologues (Orthologues) between Mouse and Human

Where may I find a list of mature miRNA names that are orthologues (homologues) between human and mouse? It has to be the mature miRNA, and not just the precursor/hairpin/gene names - i.e. I need the -...
0
votes
0answers
9 views

Batch annotation with RAST

I have been looking into ways to batch annotate my bacterial genomes via RAST, however I cannot access the tutorials on blog.theseed.org as my browser prevents connection for security reasons. Does ...
0
votes
1answer
59 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 ...