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[Fwd: please help how to find total number of genes in various TIGR genomes]

Hannick, Linda lhannick at tigr.org
Fri Mar 12 13:27:37 PST 2004


Hi Linda,
The current count of genes for chromosome 2 of T. brucei is 708 if you
count the pseudogenes, and 665 if you do not count the pseudogenes.  The
reason it is so much lower is that there were a number of overlapping
areas with "gene synonyms" that have since been properly accounted for.

Linda

~~~~~~~~~~~~~~~~~~~~~~~~~~~
Linda I. Hannick, Ph.D.
Bioinformatics Analyst
The Institute for Genomic Research
301-795-7857 voice
301-838-0228 fax



> -----Original Message-----
> From: Gwinn, Michelle L. 
> Sent: Friday, March 12, 2004 3:57 PM
> To: linda mcmahan; Gwinn, Michelle L.; Hannick, Linda
> Subject: Re: [Fwd: please help how to find total number of 
> genes in various TIGR genomes]
> 
> 
> 
> Hi,
> 
> I don't know the answer to that - I only work on prokaryotic 
> organisms - 
> I am cc'ing Linda Hannick, she works on the eukaryotic 
> projects and can 
> give you that information.
> 
> Best regards,
> Michelle
> 
> 
> 
> linda mcmahan wrote:
> 
> > Hi Michelle,
> >
> > Thank you very much for your prompt assistance!  Could you please
> > help  me to clarify one more thing, how do I find the total 
> number of 
> > genes  on Tbrucei chromosome 2 used to created the  
> > gene_association.tigr_Tbrucei_chr2 file listed at GO current 
> > annotation  ftp site.  From the tigr_Tbrucei.README file at 
> the GO ftp 
> > site, there  are 748 genes on Trypanosoma brucei chromosome 
> 2, is this 
> > the same  number as of today?  Thanks.
> >
> > Linda
> >
> > On Friday, March 12, 2004, at 02:35 PM, Michelle Giglio 
> (Gwinn) wrote:
> >
> >>
> >> Hello Linda,
> >>
> >> In answer to question #1, both chromosomes are represented in that
> >> file at GO.  You can differentiate the genes on the 
> chromosomes by  
> >> their locus ids (found in columns 2 and 3 of the 
> association file).   
> >> Genes on the large chromosome all start with "VC" the 
> genes on the  
> >> small chromosome all start with "VCA".
> >>
> >> Regarding question 2, that organism is Bacillus antrhacis.  I now
> >> realize, looking at the names of the files in the GO ftp 
> site, that  
> >> they are not very clear.  I had generally paid attention to the 
> >> names  as they appear in the annotations table on the GO web page, 
> >> but I see  I will need to request the names of the ftp 
> files be made 
> >> more clear  as well.
> >>
> >> Let me know if you have any other questions,
> >>
> >> Michelle
> >>
> >>
> >> Tanja Davidsen wrote:
> >>
> >>> Linda -
> >>>
> >>> I am going to direct this question to Michelle Gwinn who is in
> >>> charge  of GO assignments to prokaryotic genomes.
> >>>
> >>> Michelle - do you have answers for Linda's questions?
> >>>
> >>> Thanks,
> >>> Tanja
> >>>
> >>> linda mcmahan wrote:
> >>>
> >>>> Hi Tanja,
> >>>>
> >>>> Thank your very much again for your prompt assistance.  Sorry to
> >>>> bother  you again, could you please help me to clarify
> >>>> following questions:
> >>>>
> >>>> 1) There are chromosome 1 and 2 for V.cholerae, which 
> one is used 
> >>>> to   create the gene_association.tigr_vibrio listed at GO
> >>>>      ftp site    ftp://ftp.geneontology.org/go/gene-associations?
> >>>>
> >>>> 2) what is the genome name for the 
> >>>> gene_association_tigr_anthracis   listed at GO ftp site:  
> >>>> ftp://ftp.geneontology.org/go/gene-associations?
> >>>>
> >>>> Thanks again.
> >>>>
> >>>> Linda
> >>>>
> >>>> On Friday, March 12, 2004, at 11:15 AM, Tanja Davidsen wrote:
> >>>>
> >>>>> Linda -
> >>>>>
> >>>>> V.cholerae was used to generate the data at the GO site.
> >>>>>
> >>>>> Information on Arabidopsis can be found at:
> >>>>>
> >>>>> http://www.tigr.org/tdb/e2k1/ath1/
> >>>>>
> >>>>> I am not sure if they have a gene count, but I know you can
> >>>>> download  the data.  There is also an email contact on the  
> >>>>> Arabidopsis pages  that should be able to help you find 
> what you  
> >>>>> need.
> >>>>>
> >>>>> -Tanja
> >>>>>
> >>>>> linda mcmahan wrote:
> >>>>>
> >>>>>> Hi Tanja,
> >>>>>>
> >>>>>> Thank you very much for your prompt assistance.  Could you 
> >>>>>> please   help  me with the following additional questions:
> >>>>>>
> >>>>>> 1) Could you please direct me to the right place at 
> the TIGR web  
> >>>>>> site   where I can find total number of genes within
> >>>>>>      Arabidopsis thaliana?
> >>>>>>
> >>>>>> 2) There are vibrio cholerae, vibrio parahaemolyticus, and 
> >>>>>> vibrio    vulnificus at the TIGR web site, which one 
> is used to 
> >>>>>> create
> >>>>>> the gene_association.tigr_vibrio listed at GO ftp site      
> >>>>>> ftp://ftp.geneontology.org/go/gene-associations?
> >>>>>>
> >>>>>> Thanks again.
> >>>>>>
> >>>>>> Linda
> >>>>>>
> >>>>>>
> >>>>>> On Thursday, March 11, 2004, at 02:58 PM, Tanja Davidsen wrote:
> >>>>>>
> >>>>>>> Linda -
> >>>>>>>
> >>>>>>> Use this tool (available off of the front page of the CMR as 
> >>>>>>> DNA    Molecule Information    
> >>>>>>> <http://www.tigr.org/tigr-scripts/CMR2/DNA_mol_form.spl>):
> >>>>>>>
> >>>>>>> http://www.tigr.org/tigr-scripts/CMR2/DNA_mol_info.spl
> >>>>>>>
> >>>>>>> You can choose whichever organisms you are interested 
> in and it  
> >>>>>>> will   give you the summary of the DNA molecules from those  
> >>>>>>> genomes  including  gene counts.
> >>>>>>>
> >>>>>>> I hope this helps!
> >>>>>>>
> >>>>>>> Sincerely,
> >>>>>>> Tanja Davidsen
> >>>>>>>
> >>>>>>> Bob Dodson wrote:
> >>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> 
> ---------------------------------------------------------------
> >>>>>>>> --
> >>>>>>>> --- -- --
> >>>>>>>>
> >>>>>>>> Subject:
> >>>>>>>> please help how to find total number of genes in 
> various TIGR   
> >>>>>>>> genomes
> >>>>>>>> From:
> >>>>>>>> linda mcmahan <lmcmahan at Princeton.EDU>
> >>>>>>>> Date:
> >>>>>>>> Thu, 11 Mar 2004 14:49:37 -0500
> >>>>>>>> To:
> >>>>>>>> cmr at tigr.org
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Could you please help me with the following questions:
> >>>>>>>>
> >>>>>>>> How do I find the total number of genes in various TIGR 
> >>>>>>>> genomes   from  the TIGR web site?
> >>>>>>>>
> >>>>>>>> Thanks.
> >>>>>>>>
> >>>>>>>> Linda
> >>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> >
> 
> 


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