• MRS features

MRS divides the screen in multiple sections.

Figure 33. The MRS 'facilities'. The MRS lay-out changes every so many year a bit to allow for more features, better use of browser options, etc, so this picture is likely not entirely correct, but you will understand, I am sure.

• 'Home' brings you back to the start page of MRS. That is the page from which you can do keyword searches.
• 'Blast' brings you to the MRS-page from which you can do Blast searches.
• 'Align' brings you to the MRS-page from which you can do a sequence alignment.
• 'Status' lists all databases that MRS can search in. Once you are searching in a database this button will change a bit and indicate which database you are querying.

Overview of indexed databases

Click on 'Status' to get a list of databases indexed in MRS. In this long list, you find SwissProt. SwissProt can also be called Sprot, SP, etc. You sometimes need some fantasy when you work with computers...

Question 4: How many sequences does the SwissProt database contain?

Now click on SwissProt in this table and you will see the details of SwissProt inside MRS. In the table you see a column labeled 'id'. If you keep clicking further, deeper into MRS, things rapidly become adiminstrator-specific mumbo-jumbo...

Question 5: You know that in SwissProt files all lines start with a keyword of two letters. Which two-letter keyword is used for the accession number in SwissProt?

Question 6: Search in SwissProt with 'ac:P0778*', and look at the accession codes of the hits. Do you understand?

Question 7: Search in SwissProt with 'ac:P0124*', and look at the accession codes of the hits. Do you understand?

EU name: MRS05B

Extended search

You already made a search like 'ac:P0124*'. It is not difficult to guess that that search looks for entries with an accession code that starts with P0124. The extended search facility allows you to do combined searches. For example, you can search for all SwissProt bovine files with accession code starting with P1234 by selecting 'ac:P1234*' and 'os:bovine' for the second:

Searching for accession code P1234* in the species bovine.

Warning. Try to be restrictive with wildcards (asterixes) because a search with a wildcard takes much more time, and will thus be a much bigger burden to the MRS computer than a simple search without a wildcard. Four searches with wildcards running at the same time is about the upper limit of the MRS-computer.

Clearly, 'ac:' tells MRS to look for accession codes, and 'os:' to look for species. But how are you supposed to know that? Well, lets go to the list of databanks again. Go to the SwissProt info (by clicking on sprot or SwissProt). And near the bottom you see a table. In this table you see in the first column somewhere the term ac and next to it you see (in the fifth column) ′Accession number′:

Figure 34. Top of the list of MRS-indexed SwissProt fields. You see that os, for example, stands for Organism Species, gn for Gene Name, etc. Further down in the list you will find ac with as description Accession number.

Question 8: Use this extended query language to search in SwissProt for Bovine sequences that have an accession code that starts with P1234. How many can you find.

By the way, MRS is rather smart, almost paranormal. After you obtained those two sequences with the query ac:P1234* os:bovine write down their sequence names, and now run the query like:P1234* bovine. Which are the first two hits? Amazing, huh?