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Use question from newbie

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  • keng9675386
    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
    Message 1 of 3 , Mar 14, 2003
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      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
    • Will Spooner
      We re also considering using SSAHA for primer analysis. The main problem is SSAHA s sensitivity for exact-matching short sequences. The important parameters
      Message 2 of 3 , Mar 18, 2003
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        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
        >
        >
        >
        > To unsubscribe from this group, send an email to:
        > ssahausers-unsubscribe@yahoogroups.com
        >
        >
        >
        > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
        >
        >
      • Ken
        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
        Message 3 of 3 , 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
          > >
          > >
          > >
          > > To unsubscribe from this group, send an email to:
          > > ssahausers-unsubscribe@yahoogroups.com
          > >
          > >
          > >
          > > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
          >
          >
          > To unsubscribe from this group, send an email to:
          > ssahausers-unsubscribe@yahoogroups.com
          >
          >
          >
          > Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
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