27Re: [ssahausers] Use question from newbie
- Mar 18, 2003Thanks for the reply. I hope to start working with this project in a month.
I'm sure you'll hear from me again once I actually start ;)
> We're also considering using SSAHA for primer analysis.
> The main problem is SSAHA's sensitivity for exact-matching short
> sequences. The important parameters are wordLength and stepLength, used in
> generating the hash table. The smaller the wordLength and stepLength, the
> more sensitive the search, but at the expense of memory usage and search
> We're currently looking at using a wordLength of 12 with a stepLength of
> 6. This configuration should guarante a hit for a 'true' alignment of
> 17+bp. The performance is reasonable (200 sequences in a few secs), but
> the in-memory hash table is large (~2GB for the human golden path).
> Hope that helps,
> Dr William Spooner whs@...
> Ensembl Web Developer http://www.ensembl.org
> On Fri, 14 Mar 2003, keng9675386 wrote:
> > Is SSAHA suitable for searching genomic sequences using PCR primers
> > (i.e. 15 to 30mers) as the querys? I'll have a couple hundred primers
> > that I'll need to check for specificity.
> > If if is suitable, are there any parameters that I should pay close
> > attention to?
> > Thanks,
> > Ken Graham
> > University of California, Davis
> > School of Medicine, Biological Chemistry
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