The "Internet" Tab of the Search window gives you the oppportunity to query gene information on the Web. To update the orf to be searched, simply click on the "Update with currently selected" button. The selected gene is marked with a red target in the 2D and 3D mode. Choose the appropriate Internet query in the table and click on the "Search WWW" button.
    A disabled "Search WWW" button means that no Internet query is currently defined. You can edit queries as described below, or import them with annotations from GeneSpring.

• The Find Tab
• The Similarity Tab

    You can add new queries by hitting the "Add" button. To modify the name of a query simply double click on its name in the table. To modify the query description, simply double click on its description in the table. If your query needs to use the orf of the gene, fill the orf part in the query with <systematic> as shown in the following sample. When running the query, ArrayMiner will replace <systematic> with the orf identifier.

http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=SC<systematic>&form=6&db=s&Dopt=g

    If you need to use the GenBank ID of the gene in your query, fill the appropriate part with "<genbank>", as shown in the following example.When running the query, ArrayMiner will replace <genbank> with the GenBank ID of the orf.

http://www.ncbi.nlm.nih.gov/cgi-bin/UniGene/query?ORG=Rn&TEXT=<genbank>&submit=Go&ORG=Rn

    If needed, you can use multiple <genbank> and <systematic> flags in the same query. If you are using GeneSpring and had configured the Internet queries in GeneSpring, you can use the Refresh Annotations option in GeneSpring's external program interface to automatically generate this table (the queries are imported with annotations). This will also fill the GenBank accession numbers if available. You can also directly generate a tsv file (Tab Separated Values) to generate this table as explained in the next section.

    Creating the Internet query database from a text file :

    If you are running ArrayMiner as a standalone tool, you need to specify in a tsv file (Tab Separated Values), the engines and queries you want to use, in the following format :

• One search engine per line.
• For each search engine, the name of the engine, followed by the corresponding http query. To specify the part of the http query that corresponds to the ID of the gene, simply begin this part with a '<' character and end it with a '>' character, as shown in the following example.

• Name the file "AMSearchDB.tsv" and save it in the ArrayMiner directory (i.e. in the same folder as the executable) Note that Macintosh users should save the file in the bin folder of the ArrayMiner folder. You can use any text editor program to perform this operation (for example the Wordpad if you are running on a PC computer).