Updating databases in

02-Dec-2015 06:03 by 7 Comments

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2016-12-25-11-11-11.xml) and copy it to your Mascot directory.Do not over-write the original databases_1or libraries_1files.

This means that, for databases such as Swiss Prot and NCBIprot, all you need do to make a new sequence database available for searching in Mascot is: When a new database is created, unless it is predefined, you will either need to supply download URLs for the files or copy the files manually to the specified directory on the Mascot Server before configuration can be completed.

In this case, the whole system will slow down and the hard disk will be observed to be “thrashing”. Threads: A Mascot search can use multiple threads, so as to make use of all the logical processors covered by the licence.

Usually, it is best to leave threads set to -1, which means automatic.

The following terms may benefit from additional explanation: Database Name: Each database must have a unique name. Note that these names are case sensitive, and much confusion can be caused by creating both Swiss Prot and swissprot.

Local paths: The delimiters between directories must always be forward slashes, even if Mascot is running on a Windows system.

The default parent directory for sequence database directories can be specified on the Settings page.

Memory mapping and locking: Memory mapped files can be locked in memory, but only if the computer has sufficient RAM.

When a new database is added, the sequence directory specifies the default path under which the database directory will be created unless it already exists.

This is only a default, and you can change the path during configuration of a database.

When a library is created from search results, only results files and peptide matches that pass suitable filtering criteria will be included in the library.

More information about spectral library filters can be found on the Spectral library search help page.

This is primarily to allow parse rules to be tested, but it also verifies that the download URL works or that the manually copied files have the correct names and security settings / permissions.

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