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# The Planarian 454 Dataset HTTP Site #
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DISCLAIMER:
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We do not warrant or assume any legal liability or responsibility
for the accuracy, completeness, or usefulness of any information or
process disclosed. We make no claims about the suitability or accuracy
of the sequences available here for any purpose, and makes no
warranties, either expressed or implied, including merchantability and
fitness for a particular purpose or that the use of these data will not
infringe any third party patents, copyrights, trademarks, or other
rights. Data is provided "AS IS". The materials contained in this
site can be downloaded or copied provided that ALL copies are under
the Creative Commons Attribution-Noncommercial-ShareAlike License.
Any redistribution of the data should carry this notice.

If you use data available from this web site, please cite the following paper:

   "Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea"
   Abril, Cebrià, et al, BMC Genomics, 2010, 11:731.


HTTP directory structure and file naming conventions:
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To facilitate storage and download all data are GNU Zip (gzip, *.gz)
or ZIP (zip, *.zip) compressed. So when the download is complete,
please use appropriate unzip program and decompress all the files.

README.txt :
         this file (detailed description of what directory contains).
FWD.fa & REVFWD.fa :
         ESTs from Schmidtea mediterranea NCBI UniGene set.


Files below have been produced on Skuld-Tech facilities:
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ASSEMBLAGE_PLANARIAN_90  :
         cluster/contigs construction as ACE format
         with 90 percent of similarity.
ASSEMBLAGE_PLANARIAN_98  :
         cluster/contigs construction as ACE format
         with 98 percent of similarity.
ASSEMBLAGE_PLANARIAN_90e :
         cluster/contigs construction as ACE format
         with 90 percent of similarity and
         using previous old cleaned UniGene ESTs.

consensus_planarian_98db  :
         nucleotide cluster/contigs sequences as multifasta format
         with 98 percent of similarity.
consensus_planarian_90db  :
         nucleotide cluster/contigs sequences as multifasta format
         with 90 percent of similarity.
consensus_planarian_90edb :
         nucleotide cluster/contigs sequences as multifasta format
         with 90 percent of similarity and
         using previous old cleaned UniGene ESTs.

consensus_planarian_prot_98db  :
         protein sequences as multifasta format translated
         from their corresponding cluster/contigs sequences. 
consensus_planarian_prot_90db  :
         protein sequences as multifasta format translated
         from their corresponding cluster/contigs sequences.
consensus_planarian_prot_90edb :
         protein sequences as multifasta format translated
         from their corresponding cluster/contigs sequences.


Files below have been computed on Computational Genomics Lab facilities:
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90db.ncbi_blastx_NRprot.hitdesc.tbl  :
         Results of BLASTX against NCBI NRprot
         for the GO analysis on Smed454-90db dataset.
98db.ncbi_blastx_NRprot.hitdesc.tbl  :
         Results of BLASTX against NCBI NRprot
         for the GO analysis on Smed454-98db dataset.
90edb.ncbi_blastx_NRprot.hitdesc.tbl :
         Results of BLASTX against NCBI NRprot
         for the GO analysis on Smed454-90edb dataset.

For the Gene Ontology (GO) annotation we split the following analises into
Biological Process (BP), Cellular Component (CC) and Molecular Function (MF).

consensus_planarian_90db.ncbi_blastx_NRprot.out.BP.goa
consensus_planarian_90db.ncbi_blastx_NRprot.out.CC.goa
consensus_planarian_90db.ncbi_blastx_NRprot.out.MF.goa
         GO annotation for all the sequences on Smed454-90db.

consensus_planarian_98db.ncbi_blastx_NRprot.out.BP.goa
consensus_planarian_98db.ncbi_blastx_NRprot.out.CC.goa
consensus_planarian_98db.ncbi_blastx_NRprot.out.MF.goa
         GO annotation for all the sequences on Smed454-98db.

consensus_planarian_90edb.ncbi_blastx_NRprot.out.BP.goa
consensus_planarian_90edb.ncbi_blastx_NRprot.out.CC.goa
consensus_planarian_90edb.ncbi_blastx_NRprot.out.MF.goa
         GO annotation for all the sequences on Smed454-90edb.