title: Expanded protein information at SGD: new pages and proteome browser.
abstract: The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance the depth and accessibility of protein annotations. In particular, we have expanded ongoing efforts to improve the integration of experimental information and sequence-based predictions and have redesigned the protein information web pages. A key feature of this redesign is the development of a GBrowse-derived interactive Proteome Browser customized to improve the visualization of sequence-based protein information. This Proteome Browser has enabled SGD to unify the display of hidden Markov model (HMM) domains, protein family HMMs, motifs, transmembrane regions, signal peptides, hydropathy plots and profile hits using several popular prediction algorithms. In addition, a physico-chemical properties page has been introduced to provide easy access to basic protein information. Improvements to the layout of the Protein Information page and integration of the Proteome Browser will facilitate the ongoing expansion of sequence-specific experimental information captured in SGD, including post-translational modifications and other user-defined annotations. Finally, SGD continues to improve upon the availability of genetic and physical interaction data in an ongoing collaboration with BioGRID by providing direct access to more than 82,000 manually-curated interactions.
authors.affiliation: Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305-5120, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Nash
authors.forename: Shuai
authors.initials: S
authors.lastname: Weng
authors.forename: Ben
authors.initials: B
authors.lastname: Hitz
authors.forename: Rama
authors.initials: R
authors.lastname: Balakrishnan
authors.forename: Karen R
authors.initials: KR
authors.lastname: Christie
authors.forename: Maria C
authors.initials: MC
authors.lastname: Costanzo
authors.forename: Selina S
authors.initials: SS
authors.lastname: Dwight
authors.forename: Stacia R
authors.initials: SR
authors.lastname: Engel
authors.forename: Dianna G
authors.initials: DG
authors.lastname: Fisk
authors.forename: Jodi E
authors.initials: JE
authors.lastname: Hirschman
authors.forename: Eurie L
authors.initials: EL
authors.lastname: Hong
authors.forename: Michael S
authors.initials: MS
authors.lastname: Livstone
authors.forename: Rose
authors.initials: R
authors.lastname: Oughtred
authors.forename: Julie
authors.initials: J
authors.lastname: Park
authors.forename: Marek
authors.initials: M
authors.lastname: Skrzypek
authors.forename: Chandra L
authors.initials: CL
authors.lastname: Theesfeld
authors.forename: Gail
authors.initials: G
authors.lastname: Binkley
authors.forename: Qing
authors.initials: Q
authors.lastname: Dong
authors.forename: Christopher
authors.initials: C
authors.lastname: Lane
authors.forename: Stuart
authors.initials: S
authors.lastname: Miyasato
authors.forename: Anand
authors.initials: A
authors.lastname: Sethuraman
authors.forename: Mark
authors.initials: M
authors.lastname: Schroeder
authors.forename: Kara
authors.initials: K
authors.lastname: Dolinski
authors.forename: David
authors.initials: D
authors.lastname: Botstein
authors.forename: J Michael
authors.initials: JM
authors.lastname: Cherry
mesh_terms: D003196:Computer Graphics; D030562:Databases, Protein; D016681:Genome, Fungal; D020407:Internet; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D029701:Saccharomyces cerevisiae Proteins