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Bioinformatics FAQ (Frequently Asked Questions) - Practical tips
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(Continued from previous part...)
- Use a local favourite program on the Web server of your
choice.
- Use at least two and preferably three similarity tables.
- If using Smith-Waterman or FASTA algorithms ensure that the
gap opening penalty is high enough.
- If the initial search finds no or insufficient matches repeat
it with a highly diverged matrix and/or with a
Smith-Waterman-based server.
- If this doesn't work try switching from a PAM matrix to a
BLOSUM matrix.
...I'm not sure
whether or not to use the defaults.
Hugh, David and Alexander again on when not to use the default
search parameters provided by a server.
- ...when the homologues you are looking for to match your query
are highly diverged.
- ...when the query or matches are short.
- ...when you are only interested in a specific (in the sense of
"species") subset of database matches with a particular
evolutionary relationship to your sequence of interest---a
relationship not implied by the default settings.
How can I align two
sequences?
This section will also be expanded for newbies, until then, here
are Hugh, David and Alexander's tips for alignment:
- Use an appropriately divergent matrix (I'll be adding a table
soon to explain this).
- Reduce your gap penalty relative to that you used for your
database search.
- Use the MaxSegs/Waterman-Eggert version of the dynamic
programming algorithm to provide the best local alignment and also
to search for repeats.
How can I
predict the function of a gene (product)?
[XXXX INSERT FUNCTION PREDICTION ADVICE HERE]
How can I
predict the structure of a sequence?
You could start with anyone of these excellent guides (listed
strictly in alphabetical order):
How can I
simulate a biomolecule?
Here's Peter J. Steinbach's "Introduction
to Macromolecular Simulation"
How can I write up?
Go here to
download some detailed advice. Go here for
more links.
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