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.

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6
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2answers
457 views

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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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 ...
3
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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. ...
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2answers
40 views

How to generate Genbank format out of paired end fastq data?

I've unmapped cleaned paired end sequence data in fastq format of a bacterial genome. I want to get a sequence data in Genbank format in the end. What are the exact steps that I have to follow in ...
2
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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: ...
1
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1answer
25 views

Variants in Exome that affect miRNAs related to Schizophrenia

I have 3 exomes results (VCF files), I would like to study variants (SNP, INDEL) that can affect the miRNAs, which are related to a complex disease (Schizophrenia). What is the best way to assess the ...
2
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3answers
962 views

Annotation with Prokka or RAST.

I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank (NCBI Reference Sequence: NC_003389.1). I ran those sequences on Prokka and RAST ...
1
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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 ...
3
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1answer
58 views

TRAL does not find “Phobos result file”

I want to use TRAL to annotate tandem repeats in the reference genome of Caenorhabditis elegans. For this, I need to install some external software, such as Phobos. I've downloaded Phobos and I am ...
2
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1answer
59 views

RNA seq fasta file annotation from alignment to reference matches

I've got a fasta file with some RNA seq data and another csv file with the output from plast where I've aligned it to a reference using plastn. I'm struggling with figuring out a command to append my ...
2
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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,...
5
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4answers
1k views

tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable

I have downloaded tRNAscan-SE from here. After decompressing and untaring the file, I installed it using: ./configure make make install When I type ...
3
votes
1answer
29 views

Batch detection of CRISP proteins in fasta file

Probably a naive question. I am inexperienced. I am interested in identifying potential CRISP (Cysteine-rich secretory proteins) in a certain tissue transcriptome (ca. 20k sequences in fasta). I ...
1
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1answer
377 views

Expand granges object different amounts upstream vs. downstream

I am attempting to get gene regions and their immediate neighborhoods using Bioconductor GenomicRanges packages. It is very easy for me to extend the regions around genes if I want to extend it the ...
1
vote
1answer
107 views

GFF file too big to load into R

I want to load a GFF (annotation) file into an R data frame in order to extract some information from it, e.g. the location of transposons in the genome. I used the following code: ...
1
vote
1answer
558 views

update dbSNP ID

I have used dbSNP build 138 to tag 'rs' ID in my VCF file. But later I came to know that now dbSNP build 150 has been released. I want to update the rs IDs in my VCF file. I tried but I found a ...
4
votes
1answer
609 views

get gene lines from gtf file

I would like to retrieve gene lines from a GTF file for which I only have exons & transcripts lines (output from Cufflinks) and alternative splicing possible. I need gene lines for compatibility ...
4
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1answer
238 views

Keep Format and Individual fields when annotating VCF with VEP

I'm currently updating my Variant Calling Pipeline by switching the VCF annotating software from Annovar to VEP for a variety of regions, not least how easy it is to annotate with HGVS notation and ...
2
votes
1answer
66 views

How to add data to AnnotationHub

I recently started using the Bioconductor AnnotationHub package for accessing lots of common datasets, but I've noticed that there are a lot of newer databases that have not made it into AnnotationHub'...
3
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2answers
377 views

How can I find the chromosomal location of a list of genes?

I have a list of genes nearly 20000: gene name (column1) and coordinates (columns 2 and 3) ...
3
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2answers
140 views

Generate SNP/indel annotation in Arabidopsis

I have a genome-wide list of germline SNPs and short indels for Arabidopsis thaliana, which I generated with Varscan. Regardless of the tool used to generate them, I would like to annotate them, i.e. ...
1
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1answer
27 views

Find specific functional genes from a list?

I have compiled a list of genes that are distinct from 2 different conditions. From this list (of about 600 human genes), I want to find out if any of the genes in this list have acetyl transferase ...
2
votes
2answers
248 views

seqret error when trying to transform GFF3 and FASTA files into EMBL format

I am using the tool seqret from emboss to transform an annotation file in GFF3 format and a FASTA file into an EMBL file because Wormbase does not supply an EMBL file with annotation and sequence ...
3
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1answer
47 views

Syntenic gene browser

I found that there is a Syntenic gene browser at GEvo. Do anyone know where could I find a similar browser for a local installation?
1
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1answer
223 views

How to fix 5'UTR annotation with RNA-seq data?

I am studying the transcriptome of Arabidopsis. Interestingly, the 5' UTR of the latest annotation is usually too long. Here is an example (this gene is right to left). You can see both EST (orange ...
1
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1answer
26 views

Why does RATT create a directory with chromosome sequences and how can I stop it?

I have run RATT to transfer the annotation from a reference strain to another strain. For this, I have run: ...
2
votes
1answer
78 views

Problem installing RATT

I have followed the steps here to install RATT, i.e.: svn co "https://svn.code.sf.net/p/ratt/code/" ratt-code However, when I check my installation by running '$...
1
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3answers
2k views

Finding the nearest gene to a specified gene region

I've got some data on genomic regions of interest in a bedgraph-like format from the Mus musculus [mm10] genome, and would like to find out the nearest gene to these regions. Some of the regions will ...
4
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4answers
93 views

In GFF3, annotating more than one protein-coding gene (i.e. polycistronic) contained in a eukaryotic mRNA

Below is an example of a simple GFF3 file: ...
5
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2answers
657 views

Difference between de novo transcriptome assembly methods

I have been looking around (including read the original papers) to understand what is essentially the difference between StringTie in non-reference based mode (de novo) and Trinity de novo assembly. I ...
3
votes
5answers
184 views

Import a tab-separated file with differing numbers of elements in each row; prokka output

I am using prokka to annotate a bacterial genome: prokka ecoli.fa Prokka is outputting a tab-separated file (called PROKKA_12142017.tsv) with differing numbers of ...
8
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2answers
278 views

Comparing two genome annotations

I have one-dimentional array (human genome). Also I have two annotations for it, we can think about them as different peaks (it's nucleosome and secondary structures). How can we find correlation and/...
8
votes
2answers
1k views

5'UTR and 3'UTR annotation in yeast

I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of Saccharomyces cerevisiae yeast genes. The problem is finding a ...
2
votes
1answer
68 views

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 ...
5
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3answers
3k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
2
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1answer
55 views

Differences between NetAffx Hg-U133 Plus 2.0 Annotation file versions

From what I was able to observe, the annotation files (CSV) for NetAffx Hg-U133 Plus 2.0 is updated regularly. However, from glancing at the CSV files (NA35: 2015 & NA22: 2007), I can't seem to ...
5
votes
1answer
2k views

hg38 GTF file with RefSeq annotations

I'm not sure what I'm missing, but I'm struggling to find an official hg38 GTF file with RefSeq annotations. I'd like to provide ...
6
votes
1answer
98 views

Bacterial genome annotation of a clinical isolate strain?

So I'm basically so new to this that I'm just trying to find out what tools, methods, and keywords I should go look up by myself. I have a unique strain of a bacteria. I was given RNAseq data for ...
7
votes
1answer
814 views

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 ...
9
votes
3answers
949 views

Tools to create annotated table of variants from VCF

The problem: I have a VCF file, a reference genome, and a bunch of annotations for the reference (genes, repeat regions, etc.) as GFF or BED files. What I would like is a tool that takes all of this ...
3
votes
1answer
314 views

Annovar index out of date

I'm trying to use Annovar to annotate some variants with their CADD and FATHMM scores. I've downloaded the latest versions of the software and the databases but when I run it I get an error saying the ...
6
votes
2answers
407 views

Same transcript coordinates in gtf file, different transcript ID

I have a gtf file from Ensembl, and I noticed that several "transcript" annotations have the exact same coordinates. See for instance the third and fourth transcripts ("Y74C9A.2b.1" and "Y74C9A.2b.4") ...
3
votes
4answers
433 views

Basic questions about GSEA

I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, ...
2
votes
1answer
55 views

Is Wikidata a reliable KB for genomic and drugs annotations?

I'm looking for a Linked Open Data approach to annotate a dataset with human genome and drugs information. According to the Linked Open Data cloud, there are a lot of interconnected ...
3
votes
1answer
141 views

Why do BLASTn and prokka not seem to be searching the whole fasta file?

When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome. Starting with a ....
7
votes
3answers
2k views

How to perform functional analysis on a gene list in R?

From an RNA-seq experiment I have about 17000 gene ids for 2 sample conditions arranged according to their log2 fold changes when compared to a control. I need to annotate these, but I've never done ...
7
votes
1answer
676 views

How can I create my own GO association file (gaf)?

This question is based on a question on BioStars posted >2 years ago by user jack. It describes a very frequent problem of generating GO annotations for non-model organisms. While it is based on ...
5
votes
5answers
161 views

Where is an up to date miRNA database and what happened to miRBase?

miRBase 21 was published June 26, 2014 and was still in its growth phase. Why is it not being updated anymore or the project declared officially dead? ENSEMBL also uses miRBase as a starting point (...
17
votes
6answers
2k views

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 ...
9
votes
2answers
292 views

How to transfer gff annotations in genome with extensive duplications?

Microbial genomes can contain extensive duplications. Often we'd like to transfer annotations from an annotated species to one that is newly sequenced. Existing tools (e.g. RATT, LiftOver, Kraken) ...