A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

BackgroundThe cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.ResultsThe optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).ConclusionAlignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds

Linearizing torsion classes in the Picard group of algebraic curves over finite fields

We address the problem of computing in the group of $\ell^k$-torsion rational points of the jacobian variety of algebraic curves over finite fields, with a view toward computing modular representations.Comment: To appear in Journal of Algebr

Implementation of ILLIAC 4 algorithms for multispectral image interpretation

Research has focused on the design and partial implementation of a comprehensive ILLIAC software system for computer-assisted interpretation of multispectral earth resources data such as that now collected by the Earth Resources Technology Satellite. Research suggests generally that the ILLIAC 4 should be as much as two orders of magnitude more cost effective than serial processing computers for digital interpretation of ERTS imagery via multivariate statistical classification techniques. The potential of the ARPA Network as a mechanism for interfacing geographically-dispersed users to an ILLIAC 4 image processing facility is discussed

(Psycho-)Analysis of Benchmark Experiments

It is common knowledge that certain characteristics of data sets -- such as linear separability or sample size -- determine the performance of learning algorithms. In this paper we propose a formal framework for investigations on this relationship. The framework combines three, in their respective scientific discipline well-established, methods. Benchmark experiments are the method of choice in machine and statistical learning to compare algorithms with respect to a certain performance measure on particular data sets. To realize the interaction between data sets and algorithms, the data sets are characterized using statistical and information-theoretic measures; a common approach in the field of meta learning to decide which algorithms are suited to particular data sets. Finally, the performance ranking of algorithms on groups of data sets with similar characteristics is determined by means of recursively partitioning Bradley-Terry models, that are commonly used in psychology to study the preferences of human subjects. The result is a tree with splits in data set characteristics which significantly change the performances of the algorithms. The main advantage is the automatic detection of these important characteristics. The framework is introduced using a simple artificial example. Its real-word usage is demonstrated by means of an application example consisting of thirteen well-known data sets and six common learning algorithms. All resources to replicate the examples are available online