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Questions tagged [sequence-annotation]

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0answers
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hgsql not found when running a script despite being accessible on command-line

I am working on macOS. I am following the steps described here to lift over an annotation from the reference genome of C. elegans to another assembly of C. elegans. I have run this code: ...
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1answer
38 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
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0answers
26 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 ...
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0answers
48 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 ...
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0answers
33 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: ...
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0answers
37 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 ...
2
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0answers
11 views

What is tRNAscan-SE bit score?

I have used the command-line version of tRNAscan-SE on the reference genome sequence of C. elegans to predict tRNAs. The programme outputs a table with tRNA locations, amino acid, anti codon, intro ...
1
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1answer
13 views

Where can I find the DNA sequence of the C. elegans rRNA cluster?

Where can I find the DNA sequence of the C. elegans rRNA cluster? Ideally, I would be able to do it using the command-line. I've tried using NCBI but the results are unsatisfactory. I am interested ...
3
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1answer
31 views

Is there any tools that can generating FBA model from genome sequences or proteome sequences?

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them? What I was thinking is more like to ...
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0answers
30 views

Help Adjusting Bedtools Output in R

I have been asked to write a script in R to edit, using data.frame, this .fa file that is the result from extracting gene sequences from a repeat masker coordinate file on the genome I am working with....
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0answers
27 views

Genemark tuning the --soft_mask option

I was training Genemark (v.4.30) using my usual parameters. I'm realising I'm using --soft_mask 1 while I found other folks use ...
2
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2answers
86 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 ...
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1answer
20 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
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1answer
35 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 '$...
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2answers
131 views

Software recommendation: find DNA sequence distribution over entire transcript

I would like to create a density/histogram of the distribution of a particular DNA sequence over the entire transcript using R and/or command line tools. From here, I would like to use the coordinates ...
7
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1answer
217 views

How 9th column of a gff file varies from one gene prediction algorithm to another?

GFF3 formats are tabular files with 9 fields per line, separated by tabs.First 8 fields share almost same data structure. But the 9th field varies a lot depending on the features. The last field(9th ...
4
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1answer
336 views

COG Annotation - Dealing with genes assigned to two or more COG categories

I am dealing with a list of genes which have been selected from a gene enrichment analysis. In order to see what kind of genes are overrepresented, I ran eggnog-mapper to do an orthology assignment of ...
9
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4answers
171 views

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 ...