Abstract: This disclosure describes modified methods and compositions of matter pertaining to mate pair sequencing. In an implementation of the invention, mate pair sequence data is generated without cloning in a host system. In an implementation of the invention, a nucleic acid fragment is ligated into a vector. The vector containing the inserted nucleic acid fragment is digested with a restriction endonuclease that cuts at two or more places on the insert but does not cut the vector. Following the restriction endonuclease digest, the vector with portions of the nucleic acid fragment remaining after the restriction endonuclease digestion is again ligated. This ligation connects the cut ends of the insert to each other. The re-ligated product may be sequenced to obtain sequence data for both a “right” and “left” side of the originally inserted nucleic acid fragment.

Abstract: A substance identification method includes combining substances into four or more intermediate subpools in wells of a subpool plate and repooling the intermediate subpools into a number of final screening pools based on a repooling design providing the subpooled substances in at least three different final screening pools. The repooling design determines coordinates locating well positions for the substances. Another substance identification method includes using a two-dimensional array of wells arranged in rows and a number of columns that is at least 1.5 times the rows. Substances in the wells are combined into a number of screening pools. Individual screening pools include substances from wells having a row identifier in common with one other well. A pooling design provides the pooled substances in two different screening pools. The pooling design determines coordinates locating well positions for the substances.

Abstract: This application pertains to construction of pooled biological material such as DNA, RNA, proteins and the like that are able to be screened by a wide variety of methods such as PCR (Polymerase Chain Reaction), DNA/DNA hybridization, DNA/RNA hybridization, RNA/RNA hybridization, single strand DNA probing, protein/protein hybridization and a wide variety of additional methods. Our new method for construction of pools and superpools for screening differs in that the complete set is systematically divided into a variety of smaller subsets which are then re-pooled to make the final screening pools. This pooled material can be from individual samples or a population of samples. In order to reduce the analysis time, materials and expense, the pooling of high resolution small pools in a matrix allows for a lower number of user experiments to have higher resolution (as if the researcher had analyzed the complete set of small pools).