This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools.

Centromeres are essential components of eucaryotic chromosomes. In budding yeast, up to now, 15 of the 16 centromere DNAs have been isolated. Here we report the functional isolation and characterization of CEN8, the last of the yeast centromeres missing. The centromere consensus sequence for the 16 chromosomes in this organism is presented.

The aggregation of individual preference into the collective consensus opinion is a key issue in decision-making science. Generally, the aggregation methods are based on the complete preferences from all decision makers on all decision objects. In practice, it is common that individuals can be allowed to provide their incomplete preference information constantly because adequate evaluations are...

It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods-that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the rac...

The well-known procedure implemented in ClustalW oriented on the sequence comparison was applied to structure comparison. The consensus sequence as well as consensus structure has been defined for proteins belonging to serpine family. The structure of early stage intermediate was the object for similarity search. The high values of W(sequence) appeared to be accordant with high values of W(stru...

From the §Division of Endocrinology, Department of Internal Medicine, !Protein and Nucleic Acid Research Facility and Department of Microbiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908 and the $Departamento de Endocrinologia Experimental, Instituto de Znvestigaciones Biomedicas, Consejo Superior de Investigaciones Cientificas, and Facultad de Medicina, Univer...

Saccharomyces cerevisiae is often used to produce heterologous proteins that are preferentially secreted to increase economic feasibility. We used N-glycosylation as a tool to enhance protein secretion. Secretion of cutinase, a lipase, and llama V(HH) antibody fragments by S. cerevisiae or Pichia pastoris improved following the introduction of an N-glycosylation site. When we introduced an N-gl...

Automatic recognition of promoter sequences is an important open problem in molecular biology. Unfortunately, the usual machine learning version of this problem is critically flawed. In particular, the dataset available from the Irvine repository was drawn from a compilation of promoter sequences that were preprocessed to conform to the biologists’ related notion of the corrserzsUs sequence, a ...

c © 2006 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...