visualize and recover Grapegen Affymetrix Genechip Probeset Initial page: Optimized for Mozilla Firefox 3 (recommended browser)

Transcription

1 GrapeGenDB is an application to visualize and recover Grapegen Affymetrix Genechip Probeset annotations. Initial page: Optimized for Mozilla Firefox 3 (recommended browser) INITIAL PAGE (QUERY PAGE) CNB/CSIC 1

2 First time using the new version of GrapeGenDB? Make sure the initial page is displayed correctly (the appearance should be the same as the image on the left) If not, you need to remove the temporal files stored by yyour web browser. How? In Mozilla Firefox 3 (recommended browser): Tools->Clear Private Data->put t a check mark next to the item Cache In Google Chrome: / t/ h /bi / wer.py?hl=en&answer=95582 MS Explorer: CNB/CSIC 2

3 Steps to make a query 1) Query box: enter here the id of the probeset (or list of probesets) you are interested in. The annotations for the complete probeset list can also be downloaded here. 2) Filter columns: check the columns your are interested in. Only the checked columns will appear in the results. 3) Run query: click here to execute the query and show the results according to the filtered columns. CNB/CSIC 3

4 Back to main menu: click on this icon if you wish to return to the main menu. The use of the back button of the browser is discouraged. Results are visualized in a tabulated form. A row is displayed for each probeset id entered in the initial page. A column is displayed for each checked column data in the initial page. CNB/CSIC 4

5 Grapegen probeset: Grapegen pg unique Annotation origin: probesets have been assigned to name of the queried probeset ID: ID of the transcript/transcripts hybridizing to the probeset Vitis vinifera Gene IDs from 12X annotations at the Grape Genome Browser website or otherwise to other IDs in the following precedence order: 8X > Vitis EST >G Grapegen probeset CNB/CSIC 5

6 Annotation origin: When a component of the Grapegen unique ID corresponding to a 12X or an 8X annotation is clicked in the Annotation origin column, the Grape Genome Browser (Genoscope) will open to show information for that component CNB/CSIC 6

7 Protein ID: GI identifier in Entrez Protein database. When an ID of this column is clicked, the corresponding entry in Entrez Protein is displayed CNB/CSIC 7

8 Annotation: Annotation for the gene function corresponding to the Grapegen unique ID Grapegen Functional Categories: Hierarchically organized functional classification of the Grapegen unique IDs. One Grapegen unique ID can be assigned to more than one (maximum 4) functional category Redundant probesets: List of probesets representing the same Grapegen unique ID as the query probeset CNB/CSIC 8

9 Sequence: tentative consensus EST sequence used as a model in the probeset design Alignment tools BLASTN: NCBI BLASTN. Search the NCBI nucleotide database using the nucleotidic sequence of the probeset as a query BLASTX: NCBI BLASTX. Search the NCBI protein database using the translation of the nucleotidic sequence of the probeset as a query BLASTN(vitis): NCBI BLASTN filtering to obtain only hits from Vitis BLASTX(vitis): i NCBI BLASTX filtering i to obtain only hits from Vitis i BLAT(genoscope): Alignment tool to identify similarities between probeset sequences and ORFs from the PN40024 genomic sequence deposited din the Grape Genome Browser. CNB/CSIC 9

10 : download All results displayed on the screen can be downloaded as a text-tabulated file (named results.xls by default) CNB/CSIC 10

11 Access to the previous (obsolete) version of GrapeGenDB Old version of GrapeGenDB can still be accessed from the initial page Click here in case you need to access the initial (query) page of fthe obsolete lt previous version CNB/CSIC 11