ProbeSpec

Interface
This application of ProbeSpec allows easy mapping of a small number of sequences (genes or ORFs) according to given parameters.

Parameters for execution are:

  • Probe length
  • Transcriptome file: a precompiled file including sequence and abundance of all transcripts. (yeast)
  • Gene list file: Text list of all gene/ORF names to be mapped. Each entry should appear on a separate line (example).
  • Ignore genes: Text list of all gene/ORF names to be ignored.
  • Mismatch thresholds: Sequences are divided into three categories - High, Medium, Low abundance
    • Thresholds for abundance group separation, in copies per cell (e.g. >10 - high abundance, >1 - medium abundance, all others - low abundance)
    • Thresholds for specificity mapping, as a function of the abundance group of the target and background sequences. (e.g. a probe for a transcript of low abundance has to have at least 7 mismatches against a background sequence of high abundance).

Running the application will produce an output map file for each mapped sequence.

The transcriptome sequences are read directly from a database file, no preprocessing is done prior to mapping. Notice that specificity mapping of a large number of sequences is much more efficient if the index is pre-created separately in advance. Please contact Doron Lipson for information for other mapping projects. 

 

Output Format
For each ORF, the file named ‘[genename].map’ contains the following specificity information, in tab delimited format:
  • The name of the ORF and the related gene (if available).
  • Search parameters:
    • l - probe length.
    • w - criteria for differentiation between high/medium/low abundance.
    • r - threshold values for high/medium/low abundance background.
  • Specificity information for each probe p:
    • Position of p along the ORF (0-based index).
    • For each of the high/medium/low abundance categories:
      • The distance of the probe p from all ORFs in the abundance category.
      • The name of the gene/ORF, in the abundance category, that contains the sequence most similar to p.
      • Pass(1)/Fail(0) of specificty of p in the abundance category, according to threshold values.
    • The distance of the probe p from all ORFs in the transcriptome.
    • Pass(1)/Fail(0) of overall specificity of p.
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Authors
ProbeSpec was developed by Doron Lipson and Zohar Yakhini of the Computational Biology Lab, Technion, Israel. 
Comments and questions should be directed at dlipson@cs.technion.ac.il.