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MethBase: database of DNA methylation data visualized on the UCSC Genome Browser; Minimotif Miner: database of short contiguous functional peptide motifs; Oncogenomic databases: a compilation of databases that serve for cancer research; PubMed: references and abstracts on life sciences and biomedical topics; RIKEN integrated database of mammals
The main academic full-text databases are open archives or link-resolution services, although others operate under different models such as mirroring or hybrid publishers. . Such services typically provide access to full text and full-text search, but also metadata about items for which no full text is availa
Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002, and v1.0 was released in March 2003.
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). [2] [3] [4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
The first genome browser, known as the Ensembl Genome Browser, was developed as part of the Human Genome Project by a group of researchers from the European Bioinformatics Institute (EBI). It was created with the aim of providing a complete resource for the human genome sequence, with focus on gene annotation.
The UCSC Genome Browser offers isPCR, which provides graphical as well text-file output to view PCR products on more than 100 sequenced genomes. A primer may bind to many predicted sequences, but only sequences with no or few mismatches (1 or 2, depending on location and nucleotide) at the 3' end of the primer can be used for polymerase extension.
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The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs.