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http://www.bio-itworld.com/

A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials.

Proper citation: Bio-IT World (RRID:SCR_011986) Copy   

•   Source: SciCrunch Registry

http://www.fugu-sg.org/

THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.

Proper citation: Fugu Genome Project (RRID:SCR_013014) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Genetic Codes is a summary resource of the taxonomy of each record and assignment of the correct genetic code for every entry in the GenBank database. GenBank format by historical convention displays mRNA sequences using the DNA alphabet. Thus, for the convenience of people reading GenBank records, the genetic code tables shown here use T instead of U. The following genetic codes are described here: The Standard Code The Vertebrate Mitochondrial Code The Yeast Mitochondrial Code The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code The Invertebrate Mitochondrial Code The Ciliate, Dasycladacean and Hexamita Nuclear Code The Echinoderm and Flatworm Mitochondrial Code The Euplotid Nuclear Code The Bacterial, Archaeal and Plant Plastid Code The Alternative Yeast Nuclear Code The Ascidian Mitochondrial Code The Alternative Flatworm Mitochondrial Code Blepharisma Nuclear Code Chlorophycean Mitochondrial Code Trematode Mitochondrial Code Scenedesmus Obliquus Mitochondrial Code Thraustochytrium Mitochondrial Code

Proper citation: Genetic Codes (RRID:SCR_013092) Copy   

•   Source: SciCrunch Registry

http://www.cdtdb.brain.riken.jp/CDT/Top.jsp

Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.

Proper citation: Cerebellar Development Transcriptome Database (RRID:SCR_013096) Copy   

•   Source: SciCrunch Registry

http://tubic.tju.edu.cn/deg

THIS RESOURCE IS NO LONGER IN SEVICE. Documented on August 19,2019.It hosts records of currently available essential genes among a wide range of organisms. For prokaryotes, DEG contains essential genes in more than 10 bacteria, such as E. coli, B. subtilis, H. pylori, S. pneumoniae, M. genitalium and H. influenzae, whereas for eukaryotes, DEG contains those in yeast, humans, mice, worms, fruit flies, zebra fish and the plant A. thaliana. Users can Blast query sequences against DEG, and can also search for essential genes by their functions and names. Essential gene products comprise excellent targets for antibacterial drugs. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.

Proper citation: DEG - Database of Essential Genes (RRID:SCR_012929) Copy   

•   Source: SciCrunch Registry

http://www.cybase.org.au/

Cybase is dedicated to the study of a fascinating new class of proteins that possess a cyclic backbone in which the N and C termini have been joined with a conventional amide bond. These recently characterized molecules have now been found in organisms from all kingdoms of life and given the current rate of discovery the number of sequences could soon number in the hundreds. Research in our lab is aimed at further characterizing cyclic proteins and adapting them for commercial and medicinal use. In particular we work on a class of cyclic protein named the cyclotides. These proteins are found in the plants of the Rubiaceae and Violaceae and our specific goals include: determining the role that cyclotides play in plants, discovering the mechanism of action of the wide range of biological activities displayed by the cyclotides (including anti-HIV, anti-bacterial and insecticidal activity), characterising the genetics of the cyclotides and further discovery of novel cyclotides.

Proper citation: Cybase (RRID:SCR_012925) Copy   

•   Source: SciCrunch Registry

http://yayoi.kansai.jaea.go.jp/colisnp

ColiSNP is a website made up of two databases focused on SNPS. The first database is a database of Single Nucleotide Polymorphism (SNP) located in the protein coding region, and the second is a database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region. The database of Single Nucleotide Polymorphism (SNP) located in the protein coding region is a database of Single Nucleotide Polymorphism (SNP) mapped on protein structure. Users can search the data of SNP on this web site and display the structure of protein with SNP by RasMol. The database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region is a database of Single Nucleotide Polymorphism (SNP) mapped on regulation region. Users can search genes mapped snp on regulation region.

Proper citation: ColiSNP: Database of Single Nucleotide Polymorphism (RRID:SCR_013100) Copy   

•   Source: SciCrunch Registry

http://cbbiweb.uthscsa.edu/KMethylomes/

Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.

Proper citation: Cancer Methylome System (RRID:SCR_012013) Copy   

•   Source: SciCrunch Registry

http://bioinf.uta.fi/BTKbase/

A mutation registry for X-linked agammaglobulinemia (XLA). BTKbase lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Two thirds of cases are familial, and one third of cases are believed to arise from new mutations. Mutations of the BTK gene are found in approximately 80% of patients with agammaglobulinemia. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. It includes a mutation browser, which gives users access to mutations in Bruton tyrosine kinase (BTK) protein sequences, and XLA fact file, and forms for users to submit mutation to the dataset.

Proper citation: BTKbase (RRID:SCR_013101) Copy   

•   Source: SciCrunch Registry

http://dbcat.cgm.ntu.edu.tw/

A database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.

Proper citation: DBCAT (RRID:SCR_012014) Copy   

•   Source: SciCrunch Registry

http://www.cravat.us/

A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.

Proper citation: CRAVAT (RRID:SCR_012776) Copy   

•   Source: SciCrunch Registry

http://appris.bioinfo.cnio.es/

A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.

Proper citation: APPRIS (RRID:SCR_012019) Copy   

•   Source: SciCrunch Registry

http://snp.ims.u-tokyo.ac.jp/

JSNP is a database of Japanese Single Nucleotide Polymorphisms. It includes BLAST capability, keyword search, mapping information, and other tools that allow users to gather information on SNP's. SNPs are the most common form of DNA sequence variation. They are useful polymorphic markers to investigate genes susceptible to diseases or those related to drug responsiveness. Furthermore, a small subset of SNPs directly influences to the quality and/or quantity of the gene product, and increase a risk to certain diseases and to severe side effect by drugs. Through a discovery of a large number of SNPs, we would like to contribute to identification of disease-related genes and also to establish a diagnostic method to avoid drug side-effect.

Proper citation: Japanese Single Nucleotide Polymorphisms (RRID:SCR_013076) Copy   

•   Source: SciCrunch Registry

http://www.physionet.org/physiobank/database/slpdb/

MIT-BIH Polysomnographic Database is a collection of recordings of multiple physiologic signals during sleep. Subjects were monitored in Boston''s Beth Israel Hospital Sleep Laboratory for evaluation of chronic obstructive sleep apnea syndrome, and to test the effects of constant positive airway pressure (CPAP), a standard therapeutic intervention that usually prevents or substantially reduces airway obstruction in these subjects. The database contains over 80 hours'' worth of four-, six-, and seven-channel polysomnographic recordings, each with an ECG signal annotated beat-by-beat, and EEG and respiration signals annotated with respect to sleep stages and apnea

Proper citation: MIT-BIH polysomnographic (RRID:SCR_013078) Copy   

•   Source: SciCrunch Registry

http://www.sdbonline.org/fly/aimain/1aahome.htm

The InterActive Fly is an online database of Drosophilia development and metazoan evolution. It contains information on biochemical pathways, organs, images, a cis-decoder, and EvoPrinter, a machine that allows users to identify Evolutionarily Resilient DNA Sequences.

Proper citation: Interactive Fly (RRID:SCR_012784) Copy   

•   Source: SciCrunch Registry

http://thenode.biologists.com/

The Node: a community site for development biologists

Proper citation: The Node (RRID:SCR_013071) Copy   

•   Source: SciCrunch Registry

https://omictools.com/fusiondb-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FusionDB is a database of bacterial and archaeal gene fusion events - also known as Rosetta stones. Gene-fusion events are not the only resource to determine functional links between two proteins. Similar phylogenetic profiles and conserved chromosomal co-localization can also be used as an indicator for such interactions.

Proper citation: FusionDB (RRID:SCR_013314) Copy   

•   Source: SciCrunch Registry

http://proline.bic.nus.edu.sg/dedb/

Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.

Proper citation: Drosophila melanogaster Exon Database (RRID:SCR_013441) Copy   

•   Source: SciCrunch Registry

http://spd.cbi.pku.edu.cn

A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. The 18,152 entries are classified into fourteen functional categories, including "apolipoprotein", "cytokine", "protease", "toxin", etc. To make the dataset more comprehensive, nine related datasets were also collected, such as SPDI, Riken mouse secretome, SwissProt vertebrate secreted proteins, SubLoc etc.

Proper citation: Secreted Protein Database (RRID:SCR_013448) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute.

Proper citation: MACiE (RRID:SCR_013296) Copy   

•   Source: SciCrunch Registry