Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static...

SUMMARY SPrCY is a web-accessible database which provides comparison of structure prediction results for the Saccharomyces cerevisiae genome. This web service offers the ability to search, analyze and compare the yeast structural predictions from sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mGenTHREADER) methods. AVAILABILITY The service is...

It has long been argued that algorithms that find correlated mutations in multiple sequence alignments can be used to find structurally or functionally important residues in proteins. We examined the properties of four different methods for detecting these correlated mutations. On both simple, artificial alignments and real alignments from the Pfam database, we found a surprising lack of agreem...

Since the genome sequences of wild species may provide key information about the genetic elements involved in speciation and domestication, the undomesticated soybean (Glycine soja Sieb. and Zucc.), a wild relative of the current cultivated soybean (G. max), was sequenced. In contrast to the current hypothesis of soybean domestication, which holds that the current cultivated soybean was domesti...

Resampling algorithms provide an empirical, non-parametric approach to determine the statistical significance of annotations in different experimental settings. ResA(3) (Resampling Analysis of Arbitrary Annotations, short: ResA) is a novel tool to facilitate the analysis of enrichment and regulation of annotations deposited in various online resources such as KEGG, Gene Ontology and Pfam or any...

We provide a new examination of the incentive effects of welfare rules on family structure among low-income women by emphasizing that the eligibility and benefit rules in the AFDC and TANF programs are based more on the biological relationship between the children and any male in the household than on marriage or cohabitation per se. Using data from 1996 through 2008, we analyze the effects of ...

This article examines geographic differences in the use of mental health services among Aid to Families with Dependent Children (AFDC)-eligible Medicaid beneficiaries in Maine. Findings indicate that rural AFDC beneficiaries have significantly lower utilization of mental health services than urban beneficiaries. Specialty mental health providers account for the majority of ambulatory visits for...

A pair of proteins is defined to be related by a circular permutation if the N-terminal region of one protein has significant sequence similarity to the C-terminal of the other and vice versa. To detect pairs of proteins that might be related by circular permutation, we implemented a procedure based on a combination of a fast screening algorithm that we had designed and manual verification of c...

One approach for facilitating protein function prediction is to classify proteins into functional families. Recent studies on the classification of G-protein coupled receptors and other proteins suggest that a statistical learning method, Support vector machines (SVM), may be potentially useful for protein classification into functional families. In this work, SVM is applied and tested on the c...

Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pres...