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
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
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
Thanks Josh - I added the comment as an update above. I hope that's what you meant.
This was very useful. Thank you!
WebGBrowse? http://webgbrowse.cgb.indiana.edu
Yeah, I reported ModelMaker to NCBI but it didn't seem promising.
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).
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 a gff3 file for a gene?
http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html >> useful, more detail than what I'm looking for, requires gff3 file
http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html >> 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
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what's your input ? A genbank record ?
This is the kind of problem that would be a good student project for a student or small team.
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.