by Roderic Guigó 6/6/97

In this practical we will run a genomic DNA sequence against a database of position weight matrices representing promoter elements, and will try to locate potential splice sites in the genomic sequence.

WWW DB Tools

We will use:

• SRS (at EBI or EMBL) to extract a query sequence. )
• Transfac (at GBF, to search the sequence against a database of profiles for promoter elements )
• SPL (at the Sanger Center , to find potential splice sites.)

Step 1. Extract a genomic DNA sequence from the database

• Load SRS (at EBI or EMBL) and Start the session.
• Select the EMBL database and standard query form.
• Typecds in the FtDescription(Feature) box, and tata in the FtDescription(Feature) box, then do query
• Clik on AGCHYM12 entry
• look at the entry
• clik on save
• Sequence format is fasta and view FastSeqs. Then click on save.
• Netscape (text) save on e.g. genomic.fa

Step 2.Weigth matrix based search of potential promoter elements

• Search Transfac with MatInspector (http://transfac.gbf.de/cgi-bin/matSearch/matsearch.pl)
• Select Weight-Matrix-Based search
• Cut and Paste the genomic DNA sequence.
• Search Insect Matrix Group
• Matches on the sequence

Questions

• 1. Where the annotated promoters found? Why?
• 2. Where promoter elements other than the annotated found? Why?

Step 3.Multivariate Analysis based search for potential splice sites

• Load Genomic Analysis tools at the Sanger Center (http://genomic.sanger.ac.uk)
• Select Nucleotide Sequence Analysis
• Load file the genomic DNA sequence.
• Select Drosophila and spl
• Perform Search

Questions

• 1. How many potential splice sites were detected?
• 2. Were the real splice sites detected?
• 3. Did the real splice sites score high?
• 4. How many false sites were identified?

• Select Human and spl, and repeat the analysis
• compare the results.