Abstract: Many biological data analysis problems require matching data points from different data sets. For example, high-throughput protein expression liquid chromatography and mass spectrometry (LC/MS) protocols developed generate 2-dimensional feature sets that require matching on a point-by-point basis. In these protocols, it can be useful to perform all data collection sequentially and analyze the data subsequent to lab work. This avoids the need to identify all of the components in a sample before comparing it to other samples, thus saving effort and avoiding the potential problem of missing an important component due to problems in the identification stage. Such methods can involve identifying, grouping and measuring sets of characteristic peaks in order to identify and quantify shared peptides. The present teachings provide, among other things, a method for comparing and associating multiple data sets. These methods, can be used, for example, for analyzing LC/MS runs, gel images etc.

Abstract: A method and computer-program product for sequencing nucleic acid sequences using restriction fragment maps derived from end-sequenced nucleotide fragments. The initial nucleotide sequence can be processed to form a shot-gun-data set. The present teachings employ a technique called Restriction Site Shotgun Sequencing (RSSS.) It can reduce the amount of overlap required between fragment ends while still producing a good assembly. A decrease in overlap can be achieved by using additional information in the fragments to assist in determining that two fragments overlap.