Abstract In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related RNA and protein expression patterns, has made it possible determine comprehensively how genes contribute complex phenotypes. However, for major crop plants, publicly available, standard platforms parallel analysis have been limited. We report the conception design of new 22K Barley1 GeneChip probe array, a model plants without fully sequenced genome. Array content was derived from...

A correctly designed dynamic programming algorithm can be used as a fitness function to permit the evolution of maze-like levels for use in games. This study compares multiple representations evolvable mazes including direct, well positive and negative indirect representations. The first direct representation simply specifies, with binary gene, which squares grid are obstructed. second paints maze passage is allowed only between colors that same or adjacent rainbow. developmental evolve...

The widespread use of the maize Mutator (Mu) system to generate mutants exploits preference Mu transposons insert into genic regions. However, little is known about specificity insertions within genes. Analysis 79 independently isolated Mu-induced alleles at gl8 locus established that least 75 contain insertions. terminal inverted repeats (TIRs) inserted defined three new transposons: Mu10, 11, and Mu12. A large percentage (>80%) are located in 5' untranslated region (UTR) gene. Ten...

Abstract A new genetic map of maize, ISU–IBM Map4, that integrates 2029 existing markers with 1329 indel polymorphism (IDP) has been developed using intermated recombinant inbred lines (IRILs) from the B73 × Mo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences which primers were designed, optimized marker-specific PCR conditions, and data for all markers. This gene-based will facilitate a wide variety genomic research...

Evolutionary algorithms use crossover to combine information from pairs of solutions and selection retain the best solutions. Ideally, takes distinct good features each two structures involved. This process creates a conflict: progress results crossing over with different features, but produces new that are like their parents so reduces diversity on which it depends. As evolution continues, algorithm searches smaller portion search space. Mutation can help maintain is not panacea for loss....

The iterated prisoner's dilemma is a widely used computational model of cooperation and conflict. Many studies report emergent in populations agents trained to play with an evolutionary algorithm. This study varies the representation evolving resulting levels ranging from 0% over 90%. representations this are directly encoded finite-state machines, cellularly feedforward neural networks, if-skip-action lists, parse trees storing two types Boolean functions, lookup tables, function stacks,...

Recent sequencing efforts have targeted the gene-rich regions of maize (Zea mays L.) genome. We report release an improved assembly assembled genomic islands (MAGIs). The 114,173 resulting contigs been subjected to computational and physical quality assessments. Comparisons sequences bacterial artificial chromosomes suggest that at least 97% (160 165) MAGIs are correctly assembled. Because rates which junction-testing PCR primers for survey (90-92%) amplify DNA not significantly different...

Fingerprinting is a technique for generating representation-independent functional signature game playing agent. Fingerprints can be used to compare agents across representations in an automatic fashion. The theory of fingerprints developed software that play the iterated prisoner's dilemma. Examples computing are given. This paper summarizes past results and introduces following new results. dilemma strategies represented as finite-state machines must rational functions. An example strategy...

As an ancient segmental tetraploid, the maize (Zea mays L.) genome contains large numbers of paralogs that are expected to have diverged by a minimum 10% over time. Nearly identical (NIPs) defined as paralogous genes exhibit > or = 98% identity. Sequence analyses "gene space" inbred line B73 genome, coupled with wet lab validation, revealed that, conservatively, at least approximately 1% NIP, rate substantially higher than in Arabidopsis. In most instances, both members NIP pairs expressed...

Uncovering subtypes of disease from microarray samples has important clinical implications such as survival time and sensitivity individual patients to specific therapies. Unsupervised clustering methods have been used classify this type data. However, most existing focus on clusters with compact shapes do not reflect the geometric complexity high dimensional clusters, which limits their performance.We present a cluster-number-based ensemble algorithm, called MULTI-K, for sample...

Dehydrins, plant proteins that are upregulated during dehydration stress conditions, have modular sequences can contain three conserved motifs (the Y-, S-, and K-segments). The presence order of these used to classify dehydrins into one five architectures: Kn, SKn, KnS, YnKn, YnSKn, where the subscript n describes number copies motif. In this study, an architectural phylogenetic analysis was performed on 426 dehydrin were identified in 53 angiosperm 3 gymnosperm genomes. It found angiosperms...

Intrinsically disordered proteins (IDPs) are that lack a stable 3D structure but maintain biological function. It has been frequently suggested IDPs difficult to align because they tend have fewer conserved residues compared ordered proteins, our knowledge this never directly tested. To compare the alignments of IDPs, their multiple sequence (MSAs) were assessed using two different methods. The first similarity between MSAs produced same sequences created with Clustal Omega, MAFFT, and...

This study presents a system for automatically producing puzzles use in game design. The incorporates an evolutionary algorithm that optimizes the puzzle to specified level of difficulty. fitness function uses dynamic programming compute minimum number moves required solve puzzle. Two types are explored, one is maze based on chess pieces and other colors as related by color wheel create implicit maze. able produce wide variety at levels can thus be used provides library design or variable...

Fingerprinting is a technique that permits automatic classification of strategies for playing game. In this paper, the evolution iterated prisoner's dilemma (IPD) at three different noise levels analyzed using fingerprinting and other techniques including novel quantity, evolutionary velocity, derived from fingerprinting. The results are odds with initial expectations permit detection critical difference in agents without noise. Noise during fitness evaluation places larger fraction an...

Search based procedural content generation uses search techniques to locate high-quality elements for use in games. This study specifies and tests an evolutionary-computation system generate tiles plans that decompose the problem of assembling large levels. Evolutionary computation is used as off-line tool libraries both assembly plans. Systems rapidly tile can then be levels on demand with combinatorially huge numbers available. The also introduces new fitness functions, generalizing early...

Because the bulk of maize (Zea mays L.) genome consists repetitive sequences, sequencing efforts are being targeted to its 'gene-rich' fraction. Traditional assembly programs inadequate for this approach because they optimized a uniform sampling and inherently lack ability differentiate highly similar paralogs.We report development bioinformatics tools accurate genome. This software, which is based on innovative parallel algorithms ensure scalability, assembled 730,974 genomic survey...

Abstract Estimating appropriate sample sizes to measure species abundance and richness is a fundamental problem for most biodiversity research. In this study, we explore method sampling sufficiency based on haplotype diversity in the ray-finned fishes (Animalia: Chordata: Actinopterygii). To do this, use linear regression hypothesis testing methods accumulation curves from DNA barcodes 18 of fishes, statistics platform R. We simple mathematical model estimate sample-number prediction...

Cellular automata can be used to rapidly generate complex images. This study introduces fashion-based cellular as a new representation for generating cavern-like level maps. Fashion-based are defined by competition matrix that defines the benefit given cell state of having neighbor each possible state. A simple fitness function permits this type evolved produce variety parameter is performed and maps with toroidal grid, ensuring tile. The demonstrates robustness fashion based variation...

Prisoner's dilemma is a simple game used for studying cooperation and conflict. This study evolves strategies represented by 20-state finite state machines. The resulting are difficult to analyze. It not obvious looking at diagram how machine will behave, many different machines can represent the same strategy. uses technique called fingerprinting characterize strategies. Thirty runs were done each of three population sizes up 65,536 generations saved stages evolution. A large diversity...

Recent research has shown that it is possible to design fitness functions, based on dynamic programming, allow evolutionary computation automatically generate level maps for games. In this study levels with multiple types of barriers are designed. The designed under the assumption there two agent and at least one type may ignore barrier. A specification thus creates mazes, each type, coexist in same space. these dual mazes accomplished using different functions simultaneously. For example,...