I have need of a mapping of transcripts (mRNA) versus the loci of their transcription (ORF, for instance). My interest is A. thaliana and when I visit TAIR much information is provided but I fail to see how these provided data can be rendered into the form I desire to obtain. Might readers have suggestions for the location from which such a mapping might be obtained (directly), or make suggestions as to how other data might be processed thus to generate such a mapping?
At TAIR, for each locus there is a section called "Map Links", from which you can select GBrowse (Genome Browse). Have you tried it? Would it be what you need?
http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=id:4909578;dbid=general
You can also reach GBrowse from Phytozome (www.phytozome.net), just select Arabidopsis as the species and from the displayed menu select click on GBrowse. Your locus of interest would be the reference point for search.
http://www.phytozome.net/cgi-bin/gbrowse/arabi/
Hope it helps!
biomart.org has this, if I understand what you want correctly. Got to BioPortal, and the EnsemblPlants mart has sequence and locus info.
You could try TransDecoder ( http://transdecoder.sourceforge.net/ ) to find the probable ORFs out of your transcripts if you don't already have them from a database. Then you can map your transcripts to those, or use Trinotate ( http://trinotate.sourceforge.net/ ) to get a database linking transcripts and ORFs.
What you're looking for is a GFF file which describes all gene features with respect to their locations in the genome. See it here from TAIR:
ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff
When I looked at the FASTA files, all they have is sequence data. The maps are nice but not what I want. It seems more likely that the Genome Feature File format will provide the needed correlation, of locus with transcript; I will in particular want mRNA transcript to locus correlations.
@Christian - thanks for pointing me to the GFF files.
As for TriNotate, I will look into this more as time permits.
My current effort is to understand the relationship between sequence disorder and transcript. At this early stage, it appears to me that translatable transcripts tend to come from regions of high disorder, which is perhaps a bit at odds with common sense, in that one would generally correlate a structural design (and that is much of what the genome does, provide structural design for transcripts) to a high degree of order. So, I need to identify well the areas of a case genome that correspond to known transcripts, so I can well focus my analysis of sequence disorder surrounding related loci.
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