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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.

3
votes
5answers
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 elements in each row: locus_tag …
asked Dec 14 '17 by charlesdarwin
2
votes
0answers
The way I generated the embl annotation file is by running seqret on the fasta file of C. elegans and its corresponding annotation file found in GTF format: seqret -sequence c_elegans.PRJNA13758.WS263 … Update 6th August 2018 I have also tried an alternative way of getting a C. elegans annotation in EMBL format. …
asked Aug 2 '18 by charlesdarwin
3
votes
1answer
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 usi …
asked Jul 10 '18 by charlesdarwin
5
votes
4answers
I have downloaded tRNAscan-SE from here. After decompressing and untaring the file, I installed it using: ./configure make make install When I type tRNAscan-SE --help, I get the help page: tRNAsca …
asked Jul 6 '18 by charlesdarwin
1
vote
1answer
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. …
asked May 19 '18 by charlesdarwin
2
votes
0answers
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 …
asked Jul 9 '18 by charlesdarwin
1
vote
1answer
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 tutorial. …
asked Nov 8 '18 by charlesdarwin
2
votes
1answer
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 '$RATT_HOME/start.ratt.sh', it says: …
asked Jan 25 '18 by charlesdarwin
1
vote
0answers
I cannot use the annotation because I would like to apply this tool to a non-reference version of a C. elegans genome, for which no annotation is available. …
asked Jul 18 '18 by charlesdarwin
0
votes
1answer
I want to lift over the annotation from E. coli release 29 to E. coli release 42. I have followed the steps for an annotation liftover mentioned here. … Forces whole prediction to be UTR -gtf input is GTF, stop codon is not in CDS -predTab input is already in genePredTab format -requireCDS discard genes that don't have CDS annotation
asked Apr 29 '19 by charlesdarwin
2
votes
2answers
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 together … Conversion done My EMBL file is only 1.19 GB compared to the GFF3 3.34 GB, so I probably lost a lot of annotation that is not supported by EMBL. …
asked Mar 9 '18 by charlesdarwin
3
votes
4answers
I downloaded the annotation of the C. elegans genome in GFF3 format from Ensembl. I typed the following command, hoping to get the header of the file (lines starting with #). …
asked Feb 20 '19 by charlesdarwin
2
votes
1answer
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. …
asked Nov 11 '18 by charlesdarwin
1
vote
1answer
I have run RATT to transfer the annotation from a reference strain to another strain. … For this, I have run: $RATT_HOME/start.ratt.sh embl ref.fa output/annotation/ Strain This creates several things in the working directory that I do not wish: a Sequences folder with the sequence …
asked Jan 31 '18 by charlesdarwin
5
votes
0answers
I have then run the following command: repeatmasker -s -lib RepBase23.08.fasta/celrep.ref -dir annotation/ -gff c_elegans.PRJNA13758.WS266.genomic.fa I then imported the annotation table into R. …
asked Nov 6 '18 by charlesdarwin