Search

From 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).

BioRS

The BioRS Integration and Retrieval System is used to make the PEDANT S. cervisiae analysis and various yeast-related databases accessible in a fast and convenient way. Login as guest and select 'Build new query'. Choose the appropiate database and type in your query. Avoid non-alphabetic characters and spaces, instead do sub queries (AND/OR) on the result list to search multiple terms. By clicking on the numbers in the N-column you will be linked directly to the database entry.
If you would be linked to BioRS using the EUROFAN II link in the ORFs report page, login as guest and click again on the ORFs report page link. By searching one 'EUROFAN_All_Nodes' table a list with all hits and direct links to the EUROFAN pages is generated. Further heterogeneous public and proprietary databases concerning metabolic pathways, expression analysis and cellular transport will be added soon.

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).

The FASTA program ( W.R.Pearson and D.J.Lipman (1985) "Rapid and Sensitive Protein Similarity Searches", Science 227:1435-1441 ) uses a rapid algorithm to compare DNA and protein sequences. The FASTA database is a collection of the results of the FASTA program of the entire non redundant database stored in compressed form. As new sequences are added to the database, the FASTA database is incrementally updated.

Interpreting the results of your search:
Each line of your search results begins with the code of an entry in the database, followed by the score attained by comparing the sequence of that gene or protein against the protein you specified , and then followed by the name of the gene or protein. Each sequence receives 3 scores: initn, init1, opt. If self-score is selected, you will also see the score of each protein scored against itself. The results are ordered from most similar to least similar, where the top line is the specified protein compared against itself.
If you set self-score to "yes", you may also specify a cutoff ratio of optimized score to self score. This helps you to identify short sequences that have high homology with a section of the query sequence from among the longer sequecnces with weaker homology that recieve higher optimized scores (but also higher self scores, thus lowering the ratio). No optimized score lower than 80 will be shown. Of those scores above 80, the first 100 will be displayed.

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, 325331). 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.
Two approaches aim for an overview of chromosome organisation. The 'Chromosome Tables' presentation links chromosome relevant references to a feature list which comprises information on the all individual open reading frames of a given chromosome. Features covered by this lists are the coordinates of the ORFs, their gene names, viability of disruption mutants, lengths in amino acids, codon adaptation indices, numbers of prosite motifs and transmembrane spanning regions per ORF, the MIPS protein classification, and brief Ids.

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.

The S. cerevisiae PEDANT analysis (Protein Extraction, Description and Analysis Tool) is also available from here. Try the 'List of contigs' link in the left frame of PEDANT to choose the chromosome and get to 'list of orfs'. There you will find a report page for each ORF/protein with a collection of applied bioinformatics methods as well as a DNA viewer and a protein viewer.

Tables

Complementing the information that is available for a genomic substructure, such as chromosomes, ORFs, or genetic elements, CYGD provides a number of tables and graphics which comprise information about all ORFs sharing a common attribute.

Catalogues

The wealth of complex information enclosed in the genome raises a need to categorize proteins, and to sort functionally, or structurally related proteins, or e.g. proteins that cause an equivalent phenotype in the corresponding deletion strains. MIPS has compiled a number of catalogues which use a standardized terminology and offer exactly that sorting of functionally or structurally related proteins. Moreover, together they contribute to a comprehensive view regarding a specific protein, its cellular role, and on the genetic and physiological context of this protein. Using the catalogues, yeast proteins can be browsed according to their affiliation to: a functional category, a protein complex, a protein class, a mutant phenotype, an interaction pattern, and a specific subcellular localization. Compiling the catalogues is an ongoing effort at MIPS. While the MIPS Complex-Catalogue in 1999 had been complemented by another 38 novel complexes, the MIPS Functional Categories Catalogue got even more sophisticated. The latter now comprises more than the double amount of sub- and subsub-categories (total 400) and allows precise standardized functional descriptions of a gene of interest.

Pathways

CYGD 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!

Reviews

MYGD 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!

Transcription

Transcription 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 Analysis

The 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.

See also BioRS.

Information

This site offers an information platform. First of all, you are invited to an 'Introduction to S. cerevisiae'.

The reference section covers aspects of 'How to Cite MIPS Information', offers a complete set of 'Yeast genome references', and supplies the 'Documentation of Sequence Updates'. 

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.