Annotate
Blurb
   The annotate tool allows you to append multiple types of biological information to large lists of genes, defined by Genbank accession numbers. The DragonView suite of tools can then be used to visualize your gene expression data in light of the information that you derive from the annotate tool.
Instructions

1) Choose how you want to enter your data.
2a or 2b) Upload or paste your delimited text file in the proper format.
3) Choose the types of information you would like DRAGON to provide.
4) Specify which column of your table contains Genbank accession numbers.
5) Choose your output method and then press "Submit Gene List."

1) Choose how you are going to enter your data.

I am going to upload my data using the file entry field below (Go to 2a).
I am going to
paste my data into the textbox below (Go to 2b).

2a) Upload data.
Submit a file for upload to the DRAGON server.

If you are running multiple jobs, you may wish to give an identifier here for each individual dataset to distinguish the results from one another:
2b) Paste your data into the field below.

This is a very simple example data set you can use to experiment with DRAGON. For more information on how to use datasets in DRAGON annotate see the tutorial. NOTE: It should be ok to add a header row to your data. However, that row may be deleted in the output file. We are currently implementing a way to specify a header row so that it is retained in the output. If you are getting strange errors, try deleting the header row in the file you submit.

N.B. => There is a maximum number of characters which this textarea can handle. After you paste in your data please check to see that it has not been truncated at the bottom. If you think your data set is too big and is getting truncated, use the upload feature above.

3) Choose the types of information you would like DRAGON to provide.
UniGene
Unigene Cluster ID Example: Hs.1288
Cytoband Example: 1q42.13-q42.2
Locuslink Example: 58
Expression Areas Example: Aorta, Blood, Bone, Heart, Kidney, Lung, Muscle, Omentum, Prostate, Testis, Umbilical cord vein, Whole embryo, adrenal gland, head_normal, stomach_normal
UniGene Name Example: Actin, alpha 1, skeletal muscle
SwissProt
SwissProt ID Example: P02568
Subcellular Location Example: CYTOPLASMIC
Description Example: ACTIN, ALPHA SKELETAL MUSCLE
Function Example: ACTINS ARE HIGHLY CONSERVED PROTEINS THAT ARE INVOLVED IN VARIOUS TYPES OF CELL MOTILITY AND ARE UBIQUITOUSLY EXPRESSED IN ALL EUKARYOTIC CELLS
Keywords Example: Multigene family; Structural protein; Methylation; Muscle protein; Acetylation; 3D-structure
PubMed References Example: 11859360
Amino Acid Sequence Example: MCDEDETTALVCDNGSGLVKAGFAGD
Pfam
PFAM ID Example: PF00022
Description Example: Actin
KEGG (In order to view pictures of the KEGG pathways you can go here.)
KEGG Pathway Number
Example: 00600
4) Specify the column in which your Genbank numbers are located.
Column number containing GenBank numbers (with the farthest left column being 1): (required field)
Text to use as field delimiter (assumed to be a tab "\t" if left blank): (optional)
(If possible use a tab-delimited text file, however, if you have another sort of delimiter in your file, such as a comma (.csv file), then enter a "," into this text box.)
Text to use as line delimeter (assumed newline if left blank): (optional)

(This option maybe required if you are using a Unix-based machine with a file that has Unix line delimiters.)
5) Choose the type of output you would prefer.
Output as an html table:
(You can copy and paste this type of output into a spreadsheet program such as MS Excel.)
Output to browser or save as tab-delimited text file:
(If your browser asks you whether you would like open in the browser or save to disk, you can either open in the browser, select it all and paste it into a spreadsheet program such as MS Excel or save it to a folder on your computer and then open it later in a spreadsheet program.)
Output to Email Address:
(You can enter multiple addresses separated by commas. A tab-delimited text file will be emailed to you when it is ready. This option is good for large queries such as those that contain more than 1000 genes. Make sure your mail server can handle messages that may be tens of megabytes in size.)



For certain return fields, keywords for example, there may be mutliple values. You can have every value reported on one line, or one value per line. Select multiple rows if you will use your output in the DragonView tools. Please choose one method:


Copyright 2001 Kennedy Krieger Institute