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Help - non-B DNA Motif Search Tool (nBMST)

Below is a step-by-step instruction on how to submit one or more DNA sequences to find potential non-B DNA motifs using the nBMST.

1) Go to http://nonb.abcc.ncifcrf.gov/apps/nBMST/default/.

2) Enter a valid email address. Although this is optional, it is recommended if the input sequences are large.
  • Tip: Registered users who logged in do not need to enter email address. Register here.
3) Select one or more or all non-B DNA motifs.
  • Tip:On Windows, use Ctrl or Shift key to select multiple motifs.
    On Mac, use Command or Shift key.
4) Select one of the four different ways of submitting DNA sequences.
  • Use the single sequence sample will load a fasta file containing 40523 bp ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) which is selected arbitrarily.
  • Use the multi sequence sample will load a file containing a few different fasta files for batch capability demonstration.
  • Enter a sequence allows you to copy and paste your favorite DNA sequence.
  • Upload a sequence allows you to upload your sequence. (see Fig 1)
  • Figure 1 shows how a sequence is uploaded and all the non-B DNA motifs are selected.

    a screenshot of non-B Motif Search Tools

  • Tip:In both cases, the DNA sequences:
    - must be in FASTA format.
    - can contain only 'A','C','G','T', or 'N' in either uppercase or lowercase but may contain spaces.
    - must be no larger than 20 megabytes (MB). For larger data, please contact us via the contact form or email at nonb@nih.gov.
5) Enter captcha characters and hit Submit.
  • Tip:ogged in users do not need to enter this information.
  • Turnaround time for results will vary depending on the size of the sequence(s) and the number and the type of non-B DNA motifs selected. In cases where input sequences are very large and/or if multiple motifs are selected, an email address is recommended to avoid waiting time as a notification email is sent when the job is completed.

6) The nBMST result page contains the following informationin the upper section:
    Figure 2.1 displays the upper section of nBMST result page.
    a screenshot of non-B Motif Search Tools results

  • Download all to download all the files associated with this job submission,
  • New search to perform a new search,
  • the unique Job ID,
  • Total non-B motifs found in the sequence submitted,
  • Results will be stored until to show how long the result will be stored in our system, and
  • PolyBrowse, a dynamic genome browser visualization, provides a way to view the non-B DNA-forming motifs interactively and is particularly useful when there are too many entries to be viewed in a static image.

  • Figure 2.1a displays a unique PolyBrowse created for each job submission.
    a screenshot of non-B Motif Search Tools results
The lower section includes more details of each motif:
    Figure 3 displays the lower section of nBMST result for a motif (A-phased repeat shown here).
    a screenshot of non-B Motif Search Tools results

  • View image data, see Fig 3.a
  • View tabular data, see Fig 3.b and
  • Download data

  • Figure 3.a: Clicking on "View image data" displays the graphical repesentation of motif location in overal sequence
    a screenshot of non-B Motif Search Tools results

    Figure 3.b: Clicking on "View tabular data" displays the details of the non-B motifs
    a screenshot of non-B Motif Search Tools results


7) The results can be downloaded in two ways.
  • Download all under the upper section of the overall result.
  • Download data under each motif.

Note If you have any questions or comments, please feel free to contact us.