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27Re: [ssahausers] Use question from newbie

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  • Ken
    Mar 18, 2003
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      Thanks 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 ;)
      Thanks again,
      Ken
      > 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
      > speed.
      >
      > 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,
      >
      > Will
      >
      > ---
      > 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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