Simple Way To Graph A Gene Showing Putative Promotor Region, Utr, Introns And Exons

Question

[jsto7380]

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

[Pierre Lindenbaum]

what's your input ? A genbank record ?

[Mary]

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

[Mary]

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.

Answer 1

[Jeremy Leipzig]

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

Answer 2

[Josh Herr]

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

[jsto7380]

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

[Josh Herr]

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

[Prakki Rama]

This was very useful. Thank you!

Answer 3

[Mary]

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

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

Answer 4

[Alex Reynolds]

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).