Exercise ADM2
Topic
Configure a new nucleic acid database for Mascot Server
Requirements
Administrator access to an in-house Mascot server.
Experimental
Add the h_pylori_pep database to your Mascot Server.
To download the fasta file, right-click this link: h_pylori_26695.seq.fasta, and choose Save target as or Save link as
The first few lines of the database are:
>HP0945.1 tRNA-associated protein (trl) {Helicobacter pylori 26695}
ATGAGTGGTTGTGCGTCTTCTTCGCCAACTGGCACTCTTATCACTATGGTAACGATGCCA
. . .
>HP0001 hypothetical protein {Helicobacter pylori 26695}
ATGGCGACACGAACTCAAGCCAGGGGGGCTGTGGTTGAATTGTTGTATGCGTTTGAGAGC
. . .
TTAAACGCTATCTTGGATTCTTTGAGCAAAAAGCTCACTCAAAAACCCTTGAATTGA
>HP0002 6,7-dimethyl-8-ribityllumazine synthase (ribE) [6.3.3.-] {. . .}
Test the database using the following sequence query with a no enzyme or semi-trypsin search:
813.4 seq(PLANNER)
Tips
- Suitable parse rules are already defined. You just have to select them
Questions
- How many sequences are in the database?
- How many bases are in the database?
- Do any sequences have any invalid bases?