Loytynoja, A. & Goldman ,N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Phylogeny-aware gap placement software has been developed to reduce errors in sequence alignment and evolutionary analysis as Löytynoja and Goldman [ 24].
A tree that is more consistent with our binding specificity data was also obtained using the Prank algorithm (Supplementary Figure S6), which uses phylogeny-aware gap placement and scores insertions and deletions more accurately than other alignment programs (Löytynoja and Goldman, 2005, 2008).
Having classified the reads, typical usage would be to then run Tophat and Cufflinks to perform intron-aware gapped alignments and compute gene expression.
You become acutely aware of gaps and discontinuities: between slogans and realities, between political ideals and stubborn social problems, between then and now.
As a result of my outreach, advocacy organizations and universities in Mexico now have access to more information about the consequences of sugary beverage consumption, and were made more aware of gaps in research and future possibilities for collaboration.
The decision came in a civil suit brought by the parents of 11 Dover students after the school board passed a resolution in October 2004 declaring that "students will be made aware of gaps and problems in Darwin's theory and of other theories of evolution including, but not limited to, intelligent design" (ScienceNOW, 27 September).
Clinicians are aware of gaps in the therapies they can offer.
It became easier to probe into certain topics where the observer was aware of gaps in fieldwork knowledge or in the published literature, or where there were conflicting viewpoints.
"This isn't just a company, this is a movement to make women aware of this gap, and to give them a means in their control to close this gap".
They are more aware of the gap between rich and poor.
