Databases
B2G-FAR: The Blast2GO Functional Annotation Repository
B2G-FAR is a comprehensive resource of about 2000 different species. The annotations repository contains millions of high-quality functional annotations generated for over 18.000.000 distinct protein sequences by combining the Simap Database including Protein domain information (Interpro) and the Blast2GO methodology. SIMAP is a database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes. Find more information about Simap, the Similarity Matrix of Proteins, here.
Additionally annotation for 16 model and non-model Affymetrix GeneCihps can be found here.
For all data several pre-calculated statistics on functional information is available.
more info at: http://blast2go.bioinfo.cipf.es/b2gfar
The Tropical Disease Initiative Kernel
There is an urgent need for identifying new targets for drug discovery. This urgency is even more relevant for infectious diseases affecting third-world countries, which have been historically neglected by the pharmaceutical industry. For example, only ~10% of the R&D resources have been spent on illnesses that represent the 90% of the total disease burden in the world, which translates in that just ~1% of newly developed drugs are for tropical diseases.
At the beginning of the 90s, an initial Linux kernel conceived and created by Linus Torvalds paved the way for a wealth of open and free software programs and operating systems. Here we introduce what we believe can be regarded as an initial kernel for drug discovery with the hope that it will sparkle new ways for developing drugs against organisms that cause tropical diseases. The TDI kernel (v1.0) includes 297 potential drug targets against the 10 selected genomes and is freely and publicly accessible in a World Wide Web server, which was developed with Web2.0 tools for easy dissemination of the deposited data.
more info at: http://tropicaldisease.org/kernel/
PhylomeDB
PhylomeDB is a database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships.
more info at: http://phylomedb.bioinfo.cipf.es/index.html
GeneCards® Mirror
GeneCards® is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs & compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents
more info at: http://genecards.bioinfo.cipf.es/genecards/index.shtml
SNPeffect
Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease, and other phenotypic variation.
Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutation and polymorphism is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments. The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations. In addition, SNPeffect now contains Tango2: an improved aggregation detector, and Waltz: a novel predictor of amyloid forming sequences, as well as improved predictors for regions that are recognized by the Hsp70 family of chaperones. The new PupaSuite version incorporates predictions for SNPs in silencers and miRNAs including their targets, as well as additional methods for predicting SNPs in TFBSs and splice sites. Also predictions for mouse and rat genomes have been added. In addition a PupaSuite web-service has been developed to enable data access, programmatically. The combined database holds annotations for 4965073 regulatory as well as 133505 coding human SNPs and 14935 disease mutations, and phenotypic descriptions of 43797 human proteins and is accessible via http://snpeffect.vib.be and http://pupasuite.bioinfo.cipf.es/.
more info at: http://snpeffect.vib.be/
