Chatonsky had no control of the paintings' content, but he did concoct the assembly line of programs and machines that fabricated them.
Sometimes the overlap of different sequences or contigs falls outside of the tolerance of assembly programs, and a manually merged sequence is needed.
At present, the majority of assembly programs are based on the Eulerian assembly paradigm (Idury and Waterman 1995; Pevzner et al. 2001), where a de Bruijn graph is constructed with a vertex v for every (k − 1 ) -mer present in a set of reads and an edge (v, v ′ ) for every observed k-mer in the reads with (k − 1 ) -mer prefix v and (k − 1 ) -mer suffix v ′.
Comparative studies have also shown that the effectiveness of assembly programs can vary by input data set, with no assembler consistently outperforming any other [ 42, 43].
Previously obtained sequences were assembled using the cap contig assembly program of Bioedit [ 50].
These preliminary sequence identifications were supplemented by focused searches of the assembly using the FastA collection of programs and individual sequences of interest as queries [73].
The protocol will be implemented in a web server, in the future, after extensive testing of different assembly programs, and considering the choice of specific assemblers, based on the transcriptomic dataset, as proposed by Kumar and Blaxter [ 10].
The consortium's three major centers, with their large staffs of computational biologists, did not write an assembly program of their own because they had not needed one in their pilot project, on the worm genome, and perhaps did not realize how useful such a program would be.
Inspired by "A Pattern Language," computer scientists discovered they could get more efficient and reliable results if they thought of programs as assemblies of predefined code patterns instead.
For example, Le et al. demonstrated programmed assembly of Au nanoparticles by hybridizing DNA-functionalized Au nanoparticles with pre-assembled 2D DNA scaffolds on a mica surface [173].
In addition, the sequences of each contig were aligned by using the fragment assembly program of the Wisconsin Sequence Analysis Package, and consensus sequences were generated with 90% identity for a minimum of 40 nucleotides.
