Parameters for execution are:
file: a precompiled file including sequence and abundance of all
list file: Text list of all gene/ORF names to be mapped. Each
entry should appear on a separate line (example).
genes: Text list of all gene/ORF names to be ignored.
thresholds: Sequences are divided into three categories - High, Medium, Low abundance
for abundance group separation, in copies per cell (e.g.
>10 - high abundance, >1 - medium abundance, all
others - low abundance)
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.