So, we iteratively guess its size, starting with and progressively doubling until we obtain a hitting set solution (using the above approach).
If we relax our requirements an allow other cell lines to be hit at most once we can obtain a hitting set that hits the breast cancer cell lines more (Table 5 and Figure 4).
Using the greedy algorithm we obtain a hitting set with three drugs.
In 1984, when there were 170 working collieries in Britain, employing more than 190,000 people, Mr Scargill obtained a "hit list" of mines the Thatcher government was planning to close.
Music is all about welding people into a unit and with all the touring we've been doing we're now like an eight armed cosmic octopus!" Beinhorn pushed the Chili Peppers to produce the best possible takes for each of the record's thirteen tracks with the intent of the band obtaining a hit record.
Reads obtaining a hit with an E-value lower than 1E-5 thethe vector were discarded from downstream analyses.
So CLARK- E only queries non-overlapping k-mers, and the object is assigned to the first target that obtains a hit.
The final hit rate (defined as the percentage of compounds showing inhibition greater than 50% relative to the total number of compounds) was 0.16% for the FdL assay, whereas with SAMDI, we obtained a hit rate of 0.05%.
These parameter choices will increase the time needed for the search to complete but will increase the likelihood of obtaining a hit, particularly in the case of the flank length choice, as shorter flanks are less likely to overlap sequences containing gaps between the sequences being aligned.
We note the caveat that many genes contain relatively poorly conserved regions that may fail to obtain a BLAST hit at all, causing the ortholog hit ratio to be an underestimate in these cases (Additional file 5).
