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Bioinformatics FAQ
There are a large number of bioinformatics programs available to CBRG account holders via this web site. These
examples (Frequently Asked Questions) are used to illustrate the use of these tools
in answering typical queries posed by researchers.
The major web-based tools from the CBRG are listed, here.
How do I search for short sequences (oligos) using BLAST
Program name: BLAST
Notes: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity
between sequences. When using a short query sequence (perhaps an oligo of <20bps) it is advisable to edit some of the options on the search
page to make sure that all relevant results are returned.
The following options should be changed:
| Option | Default value | Value for short query sequences |
| Word Length (W value) | (11) | 7 |
| Expect threshold (E threshold) | (10) | 1000 |
| Filter options | (on) | off |
See also:
Further reading: BLAST background
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