TAIR www.arabidopsis.org) is the official source for all Arabidopsis
sequence and annotation information. Here is a link that contains the
chromosome lengths and other genome assembly information:
Any questions regarding Arabidopsis sequence data can be sent to
curator at arabidopsis.org. Thank you very much for the interest in
including Arabidopsis data into the Bioconductor packages.
Cell and Molecular Biology Graduate Group
University of Pennsylvania School of Medicine
Philadelphia, PA 19104
email: caramw at mail.med.upenn.edu
----- Original Message -----
From: "Marc Carlson" <firstname.lastname@example.org>
To: "Samuel Wuest" <wuests at="" tcd.ie="">
Cc: bioconductor at stat.math.ethz.ch
Sent: Monday, October 6, 2008 12:11:52 PM GMT -05:00 US/Canada Eastern
Subject: Re: [BioC] Arabidopsis chromosome location mappings
The CHRLENGTHS mapping would just be a vector of all named chromosome
lengths for Arabidopsis. If we had one for arabidopsis, it would not
contain the the chromosome locations mappings for much of anything.
normally get CHRLENGTHS mapping information from UCSC, but
they don't cover Arabidosis there, so we don't have a source for this
information. But since all this is, is a named vector of the
lengths, then if you know this information, you could probably fill it
in pretty easily by just creating a named vector. Also, if you have a
recommendation for a reliable public source of this information that
considered trustworthy by the arabidopsis community for this, please
tell me about it so that we can know about it too.
If you really want the location of the start of these genes along the
chromosomes, that information (from TAIR) is present in the
ath1121501CHRLOC mapping. And if you want the ends, then you can find
those in the ath1121501CHRLOCEND mapping (but this last mapping is
found in the most recent devel packages).
Please let me know if I answered your questions,
Samuel Wuest wrote:
> Hope you're fine?
> I am trying to make whole genome plots using the geneplotter
> package/annotate package. The organism I am studying is Arabidopsis
> thaliana, and obviously the annotations are not so extensive there:
> trying to build a chromLocation object, I can't obviously do that
> It is obvious to me, that the chromosome location mappings are not
> in the Arabidopsis anntation package (see below).
> My question: is there any way of plotting Arabidopsis gene
> along a chromosome. Should I just order the GeneIds (luckily, for
> Ids one can infer the gene order along a chromosome)? Has anyone
> script for this?
> Thanks for any help, best wishes,
>> newChrClass <- buildChromLocation("ath1121501")
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
> variable "ath1121501CHRLENGTHS" was not found
>  "ath1121501" "ath1121501ACCNUM"
> "ath1121501ARACYC" "ath1121501ARACYCENZYME" "ath1121501CHR"
>  "ath1121501CHRLOC" "ath1121501ENZYME"
> "ath1121501ENZYME2PROBE" "ath1121501GENENAME" "ath1121501GO"
>  "ath1121501GO2ALLPROBES" "ath1121501GO2PROBE"
> "ath1121501MAPCOUNTS" "ath1121501MULTIHIT"
>  "ath1121501PATH" "ath1121501PATH2PROBE"
> "ath1121501PMID" "ath1121501PMID2PROBE" "ath1121501SYMBOL"
>  "ath1121501_dbInfo" "ath1121501_dbconn"
> "ath1121501_dbfile" "ath1121501_dbschema"
> R version 2.7.0 (2008-04-22)
> attached base packages:
>  tools stats graphics grDevices utils datasets
> other attached packages:
>  ath1121501.db_2.2.0 TinesATH1.db_1.0 geneplotter_1.18.0
> annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.0
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