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mapping file for chromosome based visualization

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mapping file for chromosome based visualization
Resposta
09/06/09 04:32
Would you please anyone send me an example how to prepare the mapping file for chromosome based visualization?
MapMan has autogenerated chromosomal views for Arabidopsis; I cannot open that file using available applications like excel or notepad. I hope it should be some way to generate mapping file in text format for chromosomal view of other species.

Re: mapping file for chromosome based visualization
Resposta
09/06/09 10:59 em resposta a Dear marina.
Hi,

to create your own mapping file for the chromosome based visualization you can use the following xml file format. This is the file format used for the mapping files we supply.
Copy to file name somemapping.xml and load from mapman

It can be used with or without the Species,Identifier and Link section.
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<?xml version="1.0" encoding="UTF-8"?>

<Mapping>
<Species name="arabidopsis"/>
<Identifier name="affy"/>
<Link name="TAIR" description="The Arabidopsis Information Ressource">
 <Url><![CDATA[http://www.arabidopsis.org/servlets/Search?type=general&amp;&amp;sub_type=gene&amp;action=detail&amp;method=4&amp;name=]]></Url>
</Link>
<Bin name="PS" code="1">
 <Bin name="PS.lightreaction" code="1.1">
  <Bin name="PS.lightreaction.photosystem II" code="1.1.1">
   <Bin name="PS.lightreaction.photosystem II.LHC-II" code="1.1.1.1">
    <BinItem id="248151_at" type="">
     <Text><![CDATA[At5g54270->a chlorophyll A-B binding protein / LHCII type III (LHCB3)&#124; identical to Lhcb3 protein (Arabidopsis thaliana) GI:4741952; contains Pfam profile PF00504: Chlorophyll A-B binding protein]]></Text>
     <Location chrom="5" start="22055500" end="22056794"/>
    </BinItem>
    <BinItem id="251082_at" type="">
     <Text><![CDATA[At5g01530->a chlorophyll A-B binding protein CP29 (LHCB4)&#124; identical to CP29 (Arabidopsis thaliana) GI:298036; contains Pfam profile: PF00504 chlorophyll A-B binding protein]]></Text>
     <Location chrom="5" start="208936" end="210444"/>
    </BinItem>
   </Bin>
  </Bin>
 </Bin>
</Bin>
</Mapping>

Re: mapping file for chromosome based visualization
Resposta
09/06/09 16:28 em resposta a Dear marina.
Thank you very much!
I will try