We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reprod...

To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Ge...

Molecular structure of a gene, ZmSTPK1, encoding a serine/threonine protein kinase in maize was analyzed by bioinformatic tool and its expression pattern was studied under chemical biological fertilizers. Bioinformatic analysis cleared that ZmSTPK1 is located on chromosome 10, from position 141015332 to 141017582. The full genomic sequence of the gene is 2251 bp in length and includes 2 exons. ...

The bottleneck of the large-scale data processing has made bioinformatic analyses a crucial component in life sciences workflows. The two large fields in biomedical studies, whose rapid development in the recent years has strongly depended on computational methods, are genetics and proteomics. They both are strictly linked to each other, e.g. structural organization of the genome affects the va...

This paper describes a software system using bioinformatic data recorded from a performer in real-time as a probabilistic driver for the composition and subsequent real-time generation of traditionally notated musical scores. To facilitate the generation and presentation of musical scores to a performer, the system makes use of a custom LilyPond output parser, a set of Java classes running with...

C9orf72 is associated with frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS), both of which are devastating neurodegenerative diseases. Findings suggest that an expanded hexanucleotide repeat in the non-coding region of the C9orf72 gene is the most common cause of familial FTD and ALS. Despite considerable efforts being made towards discerning the possible disease-causing me...

This document surveys the computational strategies followed to parallelize the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database searching applications, to very irregularly structured patterns (phylogenetic trees). Fineand coarse-grained parallel strategies are discussed for ...

The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules--DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformati...