Proteins are sources of many peptides with diverse biological activity. Some of them are considered as valuable components of foods and drug targets with desired and designed biological activity. We are now entering an era rich in biological data in which the field of bioinformatics is poised to exploit this information in increasingly powerful ways. There are currently many databases all over ...

A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector of structural property values. It has ...

Laboratories working with draft phase genomes have specific software needs, such as the unattended processing of hundreds of single scaffolds and subsequent sequence annotation. In addition, it is critical to follow the "movement" and the manual annotation of single open reading frames (ORFs) within the successive sequence updates. Even with finished genomes, regular database updates can lead t...

Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and ...

As hidden Markov models (HMMs) become increasingly more important in the analysis of biological sequences, so too have databases of HMMs expanded in size, number and importance. While the standard paradigm a short while ago was the analysis of one or a few sequences at a time, it has now become standard procedure to submit an entire microbial genome. In the future, it will be common to submit l...

The current trend in biology research is evolving from structural genomics to functional genomics. In the field of rice research, using an insertional mutant is a powerful method for finding gene functions. However, a well-designed database using insertional mutant data is not available yet in the area of rice functional genomics. The relevant data are widely distributed and independently manag...

The PAPAyA platform has been designed to ingest, store and process in silico large genomics datasets using analysis algorithms based on pre-defined knowledge databases with the goal to offer personalized therapy guidance to physicians in particular for cancers and infectious diseases. This new highly scalable, secure and extensible framework is deployed on a cloud-based digital health platform ...

Genome structure of P. berghei and comparative genomics (Genome databases and bioinformatics) Introduction Genome structure of P. berghei GST and EST library at the University of Florida P. berghei sequencing project, Sanger Institute P. yoelii sequencing project, TIGR Comparative genomics in Leiden Genome conservation and synteny between rodent Plasmodium species Genome conservation and synten...

Dictyostelium is an attractive model system for the study of mechanisms basic to cellular function or complex multicellular developmental processes. Recent advances in Dictyostelium genomics have generated a wide spectrum of resources. However, much of the current genomic sequence information is still not currently available through GenBank or related databases. Thus, many investigators are una...

The wealth of protein sequence and structure data is greater than ever, thanks to the ongoing Genomics and Structural Genomics projects. The information available through such efforts needs to be analysed by new methods that combine both databases. One important result of genomic sequence analysis is the inference of functional homology among proteins. Until recently sequence similarity compari...