We are going to do the same search that we performed with BLAST
(see worked example)
with the Felis catus cannabinoid receptor 1, to see how similar the
results are to those that with got with the BLAST search.
Paste your sequence into the main text-entry box in the
Fasta3 homepage.
We shall select
the Swissprot protein database against which to perform our search.
We can leave the default settings for the moment. Click "Run Fasta3".
Show FASTA FORM image
Our results will appear in the same window shortly. Since we are
searching with the same protein against the same database as in the
BLAST worked example, we can
expect that our results using BLAST and FASTA shouldn't be very
different from each other. One difference between the two programs is that we
filtered the sequence for low complexity regions. This option is not
available in Fasta.
At the top of the results page, there is a table with the summary of the FASTA run.
Show FASTA RESULT SUMMARY image
Clicking on the 'Fasta result' button gives us the complete summary details for this FASTA run,
including the size of the Swissprot database being used. It is clear from this that the version
of SwissProt being used at the EBI is different from that used at NCBI,
(283,843 sequences as compared to 252,910 sequences on 17/10/07)
which will lead to some differences in results.
Show FASTA RUN DETAILS image
On the main results page, we find the matches to our query sequence.
We still find all of the same cannabinoid receptors that
we found using BLAST, but there is some slight differences in the order in which they are presented.
This is because the searching algorithms that BLAST and FASTA use have slightly different scoring
mechanisms and the two programs also use by default different scoring matrices.
The slightly different way the two programs have of scoring matches is also reflected in
the difference in scores and e-values.
The FASTA results page has some other useful features. The 'Show Annotation' button presents
the long SwissProt entry for each of the returned matches. The 'MView' button shows a coloured
multiple alignment of all the matches. The 'Show Alignments' button presents the HSPs for each
match with the query sequence. Here we find another difference between the FASTA and BLAST programs.
BLAST simply shows the alignment of the matching regions between the query and the match. FASTA
shows part of the sequence extending on either side of the match.
Show FASTA ALIGNMENT EXAMPLE image
This can be useful to indicate
whether the sequence that we are searching with is a full-length gene or not.
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