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).
ii) 'Get Sequences'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 from Chromosomes'. 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 MYGD ftp site (more detailled description).
The sequences, MYGD 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 (mitochondrial and general overview), respectively, were integrated into MYGD. Another, larger update of chromosome III is anticipated by MIPS, a preliminary sequence is presented at our ftp site (ftp://ftp.mips.embnet.org/pub/yeast/chriii_update/, check section x) for more details)
iii) 'RNAs'This site provides an overview of information on 'Small Nuclear RNAs', 'Ribosomal RNAs', 'Transfer RNAs', and 'Other RNAs'. The Tables and Graphics section (see section vii)) contributes to a comprehensive description of RNA genes in yeast (general overview). Please note, that in addition, there is a review provided in the 'Selected Reviews' section (see section viii) for a portrait) summarizing features of 'tRNA Genes and Retroelements in the Yeast Genome'.
iv) 'Chromosome Display'Two approaches aim for an overview of chromosome organisation. The 'Tabular' 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 'Physical map'. You are able to either look at a "mini-poster" of an entire chromosome ('View the Whole Chromosome'), which displays ORFs, RNA genes, and DNA elements along a coordinate axis. Alternatively, you are able to "zoom in" by selecting a special region on a particular chromosome ('View a Chromosome Section').
v) '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.
This table summarizes information regarding numbers of main- and sub-categories, and the number of ORFs which have been assigned to the catalogues, respectively, as of September 1999.
vi) 'Pathways'MYGD 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 MYGD. Please, feel invited to contribute diagrams and working models!
vii) 'Tables and Graphics'Complementing the information that is available for a genomic substructure, such as chromosomes, ORFs, or genetic elements, MYGD provides a number of tables and graphics which comprise information about all ORFs sharing a common attribute. Tables summarize special topics taken from reviews, or contributions of members of the yeast community. For example, essential genes (912) are listed versus non-essential ones (2805). YTA proteins are graphically illustrated, and alignments of yeast centromers presented, or protein-protein interactions displayed. The current status of the interactions annotated in MYGD reveals 2458 physical and 1950 genetic interactions which together describe 1298 ORFs (as of September 99).
viii) 'Selected 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!
viii) '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.
ix) 'Functional Analysis Projects'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, SCDEGEN) have been opened to the public, and the results presented on project specific MIPS web pages have been inter-linked with MYGD.
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://ftp.mips.embnet.org/pub/yeast/' contains separate directories for the up to date chromosome DNA sequences of the yeast sequencing project. A directory 'ORF_SEQ' 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.