SearchFrom this entry site you access detailed information on a particular yeast protein or genetic element. You can get to a CYGD entry directly and quickly using the query box in the left frame (gene names or systematic codes, case insensitive).
In order to detect homologues in yeast, a BLAST (Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. (1997) Nucleic Acids Res. 25, 3389-3402.) sequence similarity search tool has been provided. The 'BLAST DNA/Protein Sequence Similarity' tool employs database sets, which include either the entire chromosome sequences (YEAST_DNA), only ORF coding sequences (YEAST_ORF_DNA), sequences of all extracted proteins (YEAST_PROT), or of six frame translations of the whole chromosomes (6_FRAME_TRANS).
Interested in getting a specific DNA fragment from coordinate x to y? Then 'Get DNA Fragments from Chromosomes' will supply exactly what you need. Moreover, you are able to 'Get Protein Sequences, ORF or EXON sequences from ORFs'. Please note, that this site is particularly suited to retrieve an individual sequence. In case you are interested to download entire chromosome DNA- or ORF-sequences, please check the CYGD ftp site.
The sequences, CYGD supplies, entirely originate from the worldwide collaboration in sequencing the yeast genome. As part of our ongoing efforts to provide accurate chromosome sequences, genomic PCR verifications are instigated in cooperation with the sequencing laboratories. Since November 1997, multiple verifications were integrated into the sequence updates of chromosomes I, II, III, VI, VII, IX, XI, and XV (documentation of updates). Sequence updates effected recalculation of automatically annotated features, and accordingly, a database update. The mitochondrial genome's sequence had been accomplished by Foury and coworkers at the end of 1998 (Foury F., Roganti T., Lecrenier N., and Purnelle B. (1998) FEBS Lett., 440, 325–331). Subsequently the characteristics of the mitochondrial chromosomal elements have been updated at MYGD. This is, information on 20 proteins, 8 questionable proteins, 3 rRNA genes, 24 tRNAs, and 13 introns encoded by the mitochondrial genome respectively, were integrated into CYGD.
Each chromosome is also presented as a graphical map by the Genome Viewer which provides you with graphical clickable maps of the 16 chromosomes and the
mitochondrial genome. Beside the ORFs all other genetic elements like Tys, tRNAs, centromeres, repeats,
pseudogenes are presented above (Watson strand) or below (Crick strand) a black line. The lower colour
represents the type of feature. ORFs are tagged by the upper colour according to our ORF classification. Clicking
on any feature will bring you directly to the feature report page. Vice versa you will be linked to the cutaway of the
corresponding chromosome by clicking on the coordinates of the ORF/feature report page.
PathwaysCYGD continues to gradually build a compendium of pathways, and further models for physiological and genetic pathways provided by the yeast community have been collected and integrated into CYGD. Please, feel invited to contribute diagrams and working models!
ReviewsMYGD supplies a number of reviews contributed by members of the yeast community. Preferentially, reviews are presented that systematically characterize a phylogenetically or functionally related group of proteins / chromosomal substructures. Please, feel invited to participate!
TranscriptionTranscription and transcriptional regulation crucially depend on characteristics of the participating DNA sequences, which thus correspond to genetic entities to be annotated. The MIPS Yeast Genome Database has dedicated a focus of interest to this topic, and offers information regarding a 'Transcriptional Map of Chromosome XI', the 'Impact of MIG1 upon the Expression of Other Genes', 'Putative Targets of the GCN4 Transcription Factor', and 'Examples of uORF-containing Leaders in S. cerevisiae'. Moreover, links to 'Expression Data on the Web' are supplied.
Functional AnalysisThe unraveling of the first entire genomic structure of a well-studied model eukaryote Saccharomyces cerevisiae S288C, started off a number of functional analysis programs which systematically addressed different aspects of genome function. By 1999, data from two of these Systematic Functional Analysis Projects co-coordinated by MIPS (EUROFAN I, EUROFAN II (05.2001), SCDEGEN) have been opened to the public, and the results presented on project specific MIPS web pages have been inter-linked with CYGD.
Search algorithms for a retrieval system providing information for different mutant phenotypes characterized by these systematic functional analysis projects have been developed and implemented by MIPS. For EUROFAN I B0, fields can be selected and combined in searches that refer to growth characteristics. These searches for differential growth rates can be refined by using other phenotypic features. Anther tool enables web visitors to select specific data subsets of systematic analysis projects for inspection. Finally, synopsis tools are available that enable browsing of all data reported by the different experiments of EUROFAN I or SCDEGEN, respectively. These specialized search tools facilitate both an overview of systematic analysis data currently available, as well as navigation between different result tables.
Experimental tools and tricks have been kindly submitted to MIPS by members of the community (thanks to them, and if you read these lines, please share your favorite methods and tricks!) and a list of Yeast relevant Web links is maintained.
Last - but not least -MIPS ftp sites are given. 'ftp://ftpmips.gsf.de/yeast/' contains separate directories for the up to date chromosome DNA sequences of the yeast sequencing project. A directory at this site provides the up to date ORFs sequences of an individual chromosome or all chromosomes in different formats (pir, fasta) and compression states.