USER GUIDE

Scp2 allows you to make numerous combinations of queries in order to help you find what you are searching. One of its features is the option of introducing only a few letters of the name you want to search and be able to display results according to the query made. This is useful for users who do not remember the exact name of the item they want to look for, but remember the start or only part of the name. The Database search engine contains two fields apart from the query field:  Organism: Allows you to choose the organism where you want to look for, the options are:     E. coli P. aeruginosa S. typhi S. typhimurium

 Options: Allows you to choose the field where you want to look for, the options are:  Gene  Product  TU  TF

QUERIES
All possible combinations of queries are listed below: 1. 2. 3. 4. E. coli + Gene: search for certain gene in Escherichia coli K12. E. coli + Product: search for certain product in Escherichia coli K12. E. coli + TU: search for certain transcription unit in Escherichia coli K12. E. coli + TF: search for certain transcriptional factor in Escherichia coli K12.

5. P. aeruginosa + Gene: search for certain gene in Pseudomonas aeruginosa. 6. P. aeruginosa + Product: search for certain product in Pseudomonas aeruginosa. 7. P. aeruginosa + TU: search for certain transcription unit in Pseudomonas aeruginosa. 8. P. aeruginosa + TF: search for certain transcriptional factor in Pseudomonas aeruginosa. 9. S. typhi + Gene: search for certain gene in Salmonella typhi. 10. S. typhi + Product: search for certain product in Salmonella typhi. 11. S. typhi + TU: search for transcription unit in Salmonella typhi. 12. S. typhi + TF: search for certain transcriptional factor in Salmonella typhi.

13. S. typhimurium + Gene: search for certain gene in Salmonella typhimurium. 14. S. typhimurium + Product: search for certain product in Salmonella typhimurium. 15. S. typhimurium + TU: search for certain transcription unit in Salmonella typhimurium. 16. S. typhimurium + TF: search for certain transcriptional factor in Salmonella typhimurium. * The user will be able to navigate between objects related to the query by links in the table displayed (See the example for riboswitch).

EXAMPLES
1.- Searching for a gene in S. typhi: 1) Change the default option E. coli to S. typhi. 2) Keep the default option gene. 3) Write the name of the gene of which you would like to know about, for this example we will use thrL. 4) Click in the “Send” bottom. 5) The results are displayed in a table with the complete information about the query you made, and links to objects related to it.

2.- Searching for a riboswitch in P. aeruginosa: 1) Change the default option E. coli to P. aeruginosa. 2) Keep the default option gene. 3) Write the name of the gene regulated by a riboswitch of which you would like to know about, for this example we will use cobC 4) Click in the “Send” bottom. 5) The results are displayed in a table with the complete information about the query you made, and links to objects related to it, one of these if for riboswitch. 6) Click in the link riboswitch id. 7) The results are displayed in a table with the complete information about the riboswitch, and a link to the small molecule that regulates it.

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