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Imágen Cambiante








WELCOME TO THE SWEETPOTATO GENE INDEX

The present Sweetpotato Gene Index results from a hybrid assembly of 454 sequencing reads of two normalized cDNA libraries, one derived from leaves, and one from stems of the sweetpotato clone Tanzania (CIP #  440160), with 22,094 EST sequences from the NCBI Genebank (http://www.ncbi.nlm.nih.gov/Genbank/ )
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How to use the Sweetpotato Gene Index
To obtain a Summary Table of the contigs and singletons of the Sweetpotato Gene Index please click at "Biomart". In the menu "CHOOSE DATABASE" select DB_SWEETPOTATO, in the menu "CHOOSE DATASET" select "Sweetpotato gene index"  and then click on "Results".

Under "View" you can define the number of contigs or singletons that should be shown in the list.

Clicking on any sequence name in the Summary Table opens a window depicting the sequence and the annotation of the contig or singleton.

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Display of the Gene Index Summary Table
Under "Attributes" define those descriptor columns you want to be shown in the Summary Table.
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Downloading the Gene Index
The gene index can be downloaded from the Summary Table using the option "Export all results to" or by downloading the following attached file (Download here ).
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Search of strings in the Gene Index
Clicking on "Filters" open a window that allows for text searches in the Gene Index.

For a text search put your search term between % signs (e.g. %sucrose%) into a field and press "Results". For %sucrose% in field "UNIREF100" "Hitdescription" will reveal a list of all contigs and singletons, where the UNIREF100 annotation text contains "sucrose". To obtain all hits, please expand the number of rows that are shown in the list under "view".
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Blast search
Click at Blast" to perform a BLASTn search with your sequence(s) in the Sweetpotato Gene Index.
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REFERENCE:
Schafleitner R, Tincopa LR, Palomino O, Rossel G, Robles RF, Alagon R, Rivera C, Quispe C, Rojas L, Solis J, Kim J-Y, Hou J, Simon R. "A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining of the assembly for gene-based microsatellite markers", BMC Genomics 2010, 11:604

The Sweetpotato Gene Index was financed by the Generation Challenge Program (http://generationcp.org/ )
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SWEETPOTATO LINKS:
International Potato Center Webpage: http://www.cipotato.org/sweetpotato/
The World Sweetpotato Atlas: https://research.cip.cgiar.org/confluence/display/wsa/Home
Priorities for sweetpotato research in developing countries: http://ddr.nal.usda.gov/bitstream/10113/7469/1/IND43939124.pdf