Question: drawing comparison gene maps between strains- synterny diagrams
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gravatar for mwanerhi  erfgtr
4.4 years ago by
United States
mwanerhi erfgtr30 wrote:

Hi

i have four strains and six genes in nucleotide and protein fasta files from each one that make an operon, i want to represent these genes on a diagram or gene graphy or synterny diagram, i have tried a few few softwares like clc workbench, snap gene, genome tools, but i could not get a good picture of all the genes in operons lfor comparison. does any body have a software that can do this? i have looked at a few answers from here Draw Gene Models From Gff3 File but all i have are fasta sequences.

sequence software error gene • 1.4k views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 4.4 years ago by mwanerhi erfgtr30

i would like to create some thing like this, http://www.nature.com/nrmicro/journal/v9/n12/fig_tab/nrmicro2653_F3.html

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by mwanerhi erfgtr30

Does any of your genomes have gff file? My guess is also that those six genes are not annotated? Majority of the publication standard software that I know require gff file.

ADD REPLYlink written 4.4 years ago by S90

all the genes have been annotated but some soft ware require gi from the ncbi but my strains are newly sequenced and annotated, am in the process of analysing them and submitting them. but i need to generate synterny diagrams allong the way.

thatnx

ADD REPLYlink written 4.4 years ago by mwanerhi erfgtr30
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