Literature DB >> 14681421

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Karen R Christie1, Shuai Weng, Rama Balakrishnan, Maria C Costanzo, Kara Dolinski, Selina S Dwight, Stacia R Engel, Becket Feierbach, Dianna G Fisk, Jodi E Hirschman, Eurie L Hong, Laurie Issel-Tarver, Robert Nash, Anand Sethuraman, Barry Starr, Chandra L Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, J Michael Cherry.   

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new resources that allow the comparison and integration of information on a genome-wide scale, enabling the user not only to find detailed information about individual genes, but also to make connections across groups of genes with common features and across different species. The Fungal Alignment Viewer displays alignments of sequences from multiple fungal genomes, while the Sequence Similarity Query tool displays PSI-BLAST alignments of each S.cerevisiae protein with similar proteins from any species whose sequences are contained in the non-redundant (nr) protein data set at NCBI. The Yeast Biochemical Pathways tool integrates groups of genes by their common roles in metabolism and displays the metabolic pathways in a graphical form. Finally, the Find Chromosomal Features search interface provides a versatile tool for querying multiple types of information in SGD.

Entities:  

Mesh:

Substances:

Year:  2004        PMID: 14681421      PMCID: PMC308767          DOI: 10.1093/nar/gkh033

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  10 in total

1.  The MetaCyc Database.

Authors:  Peter D Karp; Monica Riley; Suzanne M Paley; Alida Pellegrini-Toole
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

3.  The Pathway Tools software.

Authors:  Peter D Karp; Suzanne Paley; Pedro Romero
Journal:  Bioinformatics       Date:  2002       Impact factor: 6.937

4.  Multiple sequence alignment with the Clustal series of programs.

Authors:  Ramu Chenna; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J Gibson; Desmond G Higgins; Julie D Thompson
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

5.  Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Authors:  Selina S Dwight; Midori A Harris; Kara Dolinski; Catherine A Ball; Gail Binkley; Karen R Christie; Dianna G Fisk; Laurie Issel-Tarver; Mark Schroeder; Gavin Sherlock; Anand Sethuraman; Shuai Weng; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 6.  Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.

Authors:  S F Altschul; E V Koonin
Journal:  Trends Biochem Sci       Date:  1998-11       Impact factor: 13.807

Review 7.  Issues in searching molecular sequence databases.

Authors:  S F Altschul; M S Boguski; W Gish; J C Wootton
Journal:  Nat Genet       Date:  1994-02       Impact factor: 38.330

8.  Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

Authors:  Paul Cliften; Priya Sudarsanam; Ashwin Desikan; Lucinda Fulton; Bob Fulton; John Majors; Robert Waterston; Barak A Cohen; Mark Johnston
Journal:  Science       Date:  2003-05-29       Impact factor: 47.728

9.  Sequencing and comparison of yeast species to identify genes and regulatory elements.

Authors:  Manolis Kellis; Nick Patterson; Matthew Endrizzi; Bruce Birren; Eric S Lander
Journal:  Nature       Date:  2003-05-15       Impact factor: 49.962

10.  Database resources of the National Center for Biotechnology.

Authors:  David L Wheeler; Deanna M Church; Scott Federhen; Alex E Lash; Thomas L Madden; Joan U Pontius; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Tatiana A Tatusova; Lukas Wagner
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

  10 in total
  136 in total

1.  PathBLAST: a tool for alignment of protein interaction networks.

Authors:  Brian P Kelley; Bingbing Yuan; Fran Lewitter; Roded Sharan; Brent R Stockwell; Trey Ideker
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs.

Authors:  Petr Pancoska; Zdenek Moravek; Ute M Moll
Journal:  Nucleic Acids Res       Date:  2004-08-27       Impact factor: 16.971

3.  Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.

Authors:  Amos Tanay; Roded Sharan; Martin Kupiec; Ron Shamir
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-18       Impact factor: 11.205

4.  The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.

Authors:  Andreas Ruepp; Alfred Zollner; Dieter Maier; Kaj Albermann; Jean Hani; Martin Mokrejs; Igor Tetko; Ulrich Güldener; Gertrud Mannhaupt; Martin Münsterkötter; H Werner Mewes
Journal:  Nucleic Acids Res       Date:  2004-10-14       Impact factor: 16.971

5.  Novel specificities emerge by stepwise duplication of functional modules.

Authors:  José B Pereira-Leal; Sarah A Teichmann
Journal:  Genome Res       Date:  2005-04       Impact factor: 9.043

Review 6.  Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses.

Authors:  Björn Usadel; Axel Nagel; Oliver Thimm; Henning Redestig; Oliver E Blaesing; Natalia Palacios-Rojas; Joachim Selbig; Jan Hannemann; Maria Conceição Piques; Dirk Steinhauser; Wolf-Rüdiger Scheible; Yves Gibon; Rosa Morcuende; Daniel Weicht; Svenja Meyer; Mark Stitt
Journal:  Plant Physiol       Date:  2005-07       Impact factor: 8.340

7.  A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae.

Authors:  Allegra A Petti; George M Church
Journal:  Genome Res       Date:  2005-08-18       Impact factor: 9.043

8.  Graemlin: general and robust alignment of multiple large interaction networks.

Authors:  Jason Flannick; Antal Novak; Balaji S Srinivasan; Harley H McAdams; Serafim Batzoglou
Journal:  Genome Res       Date:  2006-08-09       Impact factor: 9.043

9.  Evaluation of different biological data and computational classification methods for use in protein interaction prediction.

Authors:  Yanjun Qi; Ziv Bar-Joseph; Judith Klein-Seetharaman
Journal:  Proteins       Date:  2006-05-15

10.  Multiple bromodomain genes are involved in restricting the spread of heterochromatic silencing at the Saccharomyces cerevisiae HMR-tRNA boundary.

Authors:  Nithya Jambunathan; Adam W Martinez; Elizabeth C Robert; Nneamaka B Agochukwu; Megan E Ibos; Sandra L Dugas; David Donze
Journal:  Genetics       Date:  2005-08-03       Impact factor: 4.562

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.