Virus reference annotation

[dawn1313]

Hi,

I am trying to assemble a virus transcriptome using TopHat/Cufflinks. The reference genome is http://www.ncbi.nlm.nih.gov/nuccore/EF999921, and I wonder how I can get the annotation file (gtf/gff).

Thank you!
Dawn

[GenoMax]

You could try this script to see if it will convert genbank format file to GFF: http://www.hpa-bioinformatics.org.uk...s/snippets/115

[Chinboy]

> library(cummeRbund)
载入需要的程辑包：BiocGenerics
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载入程辑包：‘BiocGenerics’

The following objects are masked from ‘packagearallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit

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hclust

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载入需要的程辑包：GenomicRanges
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Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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载入程辑包：‘cummeRbund’

The following object is masked from ‘package:GenomicRanges’:

promoters

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promoters

The following object is masked from ‘package:BiocGenerics’:

conditions

[dawn1313]

Hi thanks for the response. Well my question is NOT the file format transfer, but how to obtain the annotation file of the virus.

Thank!
Dawn

[GenoMax]

@Dawn: I don't think your particular genome of interest is available in the list of viral genomes @NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/) so there is no ready GFF file. I was thus suggesting that you download the genbank format file for your accession from the link you had in your post and do the conversion to a GFF format file yourself.

[piet]

The reference genome is http://www.ncbi.nlm.nih.gov/nuccore/EF999921, and I wonder how I can get the annotation file (gtf/gff).

wget http://togows.dbcls.jp/entry/nucleotide/EF999921.1.gff

[dawn1313]

Thank you so much Piet and that's what I am looking for.

Best,
Dawn