Understanding nature’s mute but elegant language of living cells is the quest of modern molecular biology. From an alphabet of only four letters representing the chemical subunits of DNA emerges a syntax of life processes whose most complex expression is man. The unraveling and use of this “alphabet” to form new “words and phrases” is a central focus of the field of molecular biology. The staggering volume of molecular data and its cryptic and subtle patterns have led to an absolute requirement for computerized databases and analysis tools. The challenge is in finding new approaches to deal with the volume and complexity of data and in providing researchers with better access to analysis and computing tools to advance understanding of our genetic legacy and its role in health and disease.
The GENSCAN Web Server at MIT can be used for the identification of complete gene structures in genomic DNA.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary changes between species within the phylum Cnidaria and structures genomic and expression data to facilitate comparisons to non-cnidarian metazoans. CnidBase aims to further the progress that has already been made in the realm of cnidarian evolutionary genomics by creating a central community resource which will help drive future research and facilitate more accurate classification and comparison of new experimental data with existing data.
SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. The sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases. Additionally, the unique information on that links gene identities and sequences to the plate and well location to the library filters from the Sea Urchin genome Resource will also be presented.
Kahi Kai (‘one ocean’ in native Hawai’ian) is an online community designed to connect the oceans of the world by promoting communication and interaction between students, scientists, artists, journalists, politicians, fishermen, divers, surfers and everyone who is interested and committed to the fascinating, mysterious and endangered marine world. Join the Kahi Kai community to establish and reinforce contacts between co-workers, friends and current/future collaborators of the same domains or across disciplines. Connect to people from all around the world sharing one and the same passion…
EvoDevo publishes articles on a broad range of topics associated with the translation of genotype to phenotype in a phylogenetic context. Understanding the history of life, the evolution of novelty and the generation of form, whether through embryogenesis, budding, or regeneration are amongst the greatest challenges in biology.
All articles published by EvoDevo are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers.
Nematostella vectensis genome assembly 1.0 constructed with the JGI assembler, Jazz, includes approximately 7.8X WGS in small insert end-sequence coverage. After trimming for vector and quality, and excluding short/redundant scaffolds, there were 10,942 assembled scaffolds, containing 2,817,779 reads, and 357 Mbp of sequence. Further exclusion of contaminant and mis-assembled scaffolds reduced this to 10,804 scaffolds, with a total length of 356 Mbp Roughly half of the genome is contained in 181 scaffolds all at least 473 Kb in length.
The Metazome project organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes on the metazoan evolutionary tree. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, EnsEMBL, and JGI are hyper-linked and searchable.
This website serves as a resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods.
CreatureCast is a collaborative blog produced by members of the Dunn Lab at Brown University, along with assorted friends. This project, which is focussed on zoology in the broad sense, serves as a forum to present original content that they have produced and observations by others that they find interesting and beautiful.