SEARCH GENE INFO BULK VERIFY INFO

1. In Home page click on the site logo or the following buttons:

Start Annotator PPI

When accessing the AnnotatorPPI web server homepage you will see the fields for collecting (annotating) necessary external data, where you will be placing your data.

2. Enter your sequences

Fill up the form with the required data of the DNA sequence. Basically, you can paste your sequences into the text box. Otherwise, you can choose to upload a text FASTA file containing your DNA sequence.

The total limit for multiline sequence submissions is 50,000 letters.

You can get a quick help for each field by moving the mouse pointer over the field itself.

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When you have entered all data, just click 'Create and Annotate' (if you've pasted your data) or 'Submit file' button (if you chose to upload a FASTA file) to process your alignment, annotating and constructing prospective protein-protein interactions data.

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3. Get your results annotating

Before annotating your sequence is aligned by 'Human BLAT Search Genome'. Depending on how complex your input sequence is, the alignment can take a few seconds but no more than one minute to be fulfilled (mainly depends on the sequence length).

When the alignment is completed and all information was collected from Ensembl, Entrez, GeneCards, InterPro and UniProt databases, it will be displayed in a webpage like the following:

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To save the information to the server, click the 'Save Changes' button, to remove the data, click 'Delete' button and to upload an archive of all information to your computer, click 'Export All' button.

The exported information is packaged in a zip archive

4. Get your prospective protein-protein interactors

Click on the protein name or any ChiTaRS mutation ID to visualize the corresponding network protein-protein interactions (PPI). The following shows a network PPI for protein.

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Right-click on the network to access a menu where you can re-calculate the layout of interactors (random, tree, circle, radial type) and export the network to a graphic file.

The following shows a network PPI for the mutation (AI685149).

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Click on 'Search' to enter the AnnotatorPPI Search Gene Info

In AnnotatorPPI, a gene is defined by name and description from a variety of sources. Therefore genes may be searched by name and/or keywords:

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In AnnotatorPPI, many genes can exist for a given clone, therefore a search for a gene may result in multiple hits for the same gene name.

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By clicking on the link clone name, you can go to the verify clones webpage with the annotated information:

Annotated information

You can also search using GenAtlas:

Using GenAtlas


Click on 'Bulk Verify' in the top menu to enter the AnnotatorPPI Bulk Verify Info

After the annotation information is stored in its own database of AnnotatorPPI - a full list of AnnotatorPPI enries (sorts, i.e., a total name of the clones) will be displayed in a webpage like the following:

A full list of AnnotatorPPI enries

The table shows the statistics of all sorts. All the clones of the sort are verified by an administrator sign of 'sent'. You can get a list of clones (as 'sort name status.txt' file) for each entry by clicking on the 'LIST' blue button.

The following notations is used in the tables:

NEWNew clone
HOTHot spots
MislocMislocalized is the localization is wrong on the image
sendDBUpload into the MySQL database
SHORTThe sequence length is less than 70 bp
PolyAThere is poly(A) sequence with a length of at least 20 bp
MIXEDThere is the predicted gene(s)

By clicking on the magnifier icon beside the sort name you can access а list of clones belonging to that selected sort:

A list of clones belonging to the selected sort

From that page, by clicking on the magnifier icon beside the clone name, you can access the verify clones webpage that was earlier created with the annotated information:

The verify clone that was earlier created with the annotated information

By clicking on 'Update Info', you can update the information from all external databases for this clone.

Update the information from all external databases for this clone

By clicking on 'Export All', you can upload an zip archive of all information from all external databases for this clone.