Question: Simple Way To Graph A Gene Showing Putative Promotor Region, Utr, Introns And Exons
7
gravatar for jsto7380
6.3 years ago by
jsto738080
jsto738080 wrote:

I've been looking for a simple way to draw/graph a gene showing putative promotor region, UTR, introns and exons, hopefully with an online tool.

My previous searches on Biostar led to the following:

http://prosite.expasy.org/mydomains >> proteins

http://www.ncbi.nlm.nih.gov/projects/mapview/modelmaker.cgi?taxid=9606&contig=NT_004610.19&gene=ZNF593 >> no longer available

http://genometools.org/annotationsketch.html >> programming required

http://bio.ieo.eu/fancygene/ >> found it tricky to come up with the proper input file

http://wormweb.org/exonintron >> easiest to use, but unable to graph promoter region

I guess I'm looking for something like http://wormweb.org/exonintron that also graphs the promoter region

Anyone know of anything available?

Thanks


UPDATE:

Thanks everyone, I have to admit that I have very limited bioinformatics skills/experience: I'm not even sure what a gff3 file is. I accessed my sequences via the USCS Genome browser Like Josh, this is for a presentation

http://bio.ieo.eu/fancygene/ >> I was pasting fasta sequences which didn't work, and couldn't follow what was required from the tutorial

http://genometools.org/annotationsketch.html >> NO programming required (I saw references to programming languages and freaked out) http://genometools.org/cgi-bin/annotationsketch_demo.cgi >> how do I get a gff3 file for a gene? It wasn't clear for me following a search on this forum.

http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html >> useful, more detail than what I'm looking for, requires gff3 file

http://epigenomegateway.wustl.edu/browser >> great tool, but output graph seems would be similar to USCS output, requiring Inkscape editing

http://gsds.cbi.pku.edu.cn >> promising but my genes (calcineurin subunits) were too big http://domaindraw.imb.uq.edu.au >> for proteins

Mary, I'm interested to know what you have in mind for the student/group project

Thanks again

model gene visualization graph • 5.4k views
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by jsto738080

what's your input ? A genbank record ?

ADD REPLYlink written 6.3 years ago by Pierre Lindenbaum120k

This is the kind of problem that would be a good student project for a student or small team.

ADD REPLYlink written 6.3 years ago by Mary11k
1

Actually, that was half a thought left over from the conversation in the "News" section about BioStar directions. I suggested a place to match people with small tasks (such as: enhance exonintron to allow other display features) to people who need small student project ideas. Real life project needs + students who need some experience building/enhancing tools.

ADD REPLYlink written 6.3 years ago by Mary11k
3
gravatar for Jeremy Leipzig
6.3 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

http://genometools.org/annotationsketch.html >> programming required

no programming is required, just use the web tool and format a gff3 file with your segments

##gff-version   3
##sequence-region   ctg123 1 10000
ctg123    .    gene    1000    9000    0.5    +    .    ID=gene00001
ctg123    .    TF_binding_site    1000    1012    .    +    .    Parent=gene00001
ctg123    .    mRNA    1050    9000    .    +    .    ID=mRNA00001;Parent=gene00001
ctg123    .    mRNA    1050    9000    .    +    .    ID=mRNA00002;Parent=gene00001
ctg123    .    mRNA    1300    9000    .    +    .    ID=mRNA00003;Parent=gene00001
ctg123    .    exon    1300    1500    0.6    +    .    ID=exon1;Parent=mRNA00003
ctg123    .    exon    1050    1500    0.2    +    .    Parent=mRNA00001,mRNA00002
ctg123    .    exon    3000    3902    1    +    .    Parent=mRNA00001,mRNA00003
ctg123    .    exon    5000    5500    0.3    +    .    Parent=mRNA00001,mRNA00002,mRNA00003
ctg123    .    exon    7000    9000    1    +    .    Parent=mRNA00001,mRNA00002,mRNA00003
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Jeremy Leipzig18k
2
gravatar for Josh Herr
6.3 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

I'm not sure if these are what you are looking for (but they came in handy for me when I was preparing a presentation): Gene Structure Display Server and DomainDraw

ADD COMMENTlink written 6.3 years ago by Josh Herr5.6k
1

Thanks Josh - I added the comment as an update above. I hope that's what you meant.

ADD REPLYlink written 6.3 years ago by jsto738080

+1 Looks awesome! That will help others who have the same question!

ADD REPLYlink written 6.3 years ago by Josh Herr5.6k

This was very useful. Thank you!

ADD REPLYlink written 4.1 years ago by Prakki Rama2.2k
1
gravatar for Mary
6.3 years ago by
Mary11k
Boston MA area
Mary11k wrote:

WebGBrowse? http://webgbrowse.cgb.indiana.edu

Yeah, I reported ModelMaker to NCBI but it didn't seem promising.

ADD COMMENTlink written 6.3 years ago by Mary11k
0
gravatar for Alex Reynolds
6.3 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

The WashU Epigenome Browser contains Tracks for genomic annotation (promoters, etc.) and an Apps option to export the figure to SVG (which can be opened up and edited in Inkscape/Illustrator or converted with ImageMagick to bitmaps for documentation purposes).

ADD COMMENTlink written 6.3 years ago by Alex Reynolds28k
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