SGD Help: All Associated Sequences

Contents

Description
Accessing All Associated Sequences
Using All Associated Sequences
Other Relevant Links
Glossary Terms

Description

The All Associated Sequences page is a compendium of all Saccharomyces cerevisiae sequence entries for any allele or strain found in various external databases. To provide SGD users with accurate links to related yeast ORF entries in UniProt, EMBL, and Entrez, most mappings listed in the table were obtained from the Genome Reviews resource at the European Bioinformatics Institute. Links to MIPS were generated by using the MIPS database ID in the MIPS search program.

Accessing All Associated Sequences

All Associated Sequences for a given locus can be accessed from the appropriate Locus Summary, by using the Retrieve Sequences pull-down on the right side of the page, and from the "All Associated Seq" link in the External Links section, which is found near the bottom of the page beneath Sequence Information.

Using All Associated Sequences

The results page summarizes sequence IDs and the source databases in a table format. To retrieve sequence records, simply click on the Sequence ID to go to the appropriate site:

MIPS
Munich Information for Protein Sequences is the coordinator of the European Commission Genome Projects. The MIPS link seen on the All Associated Sequences results page connects to the appropriate ORF page at MIPS.
DNA accession ID
DNA accession ID's come from the Entrez Nucleotide database, a collection of sequences from several sources, including GenBank, RefSeq, and PDB.
Protein version ID
Protein version ID's come from the Entrez Protein search and retrieval system, and have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank.
RefSeq Protein version ID
RefSeq protein version ID's come from the NCBI Reference Sequences collection which provides a non-redundant set of DNA, RNA, and protein sequences for major research organisms. RefSeq entries for Saccharomyces cerevisiae are derived from SGD, and so should be identical to the 'reference' sequences stored at SGD. Note that other non-RefSeq sequences on the page may or may not represent other versions of the protein, which may differ from the SGD reference sequence due to allele or strain differences.
UniParc ID
UniParc ID's come from the UniProt ARChive, a comprehensive non-redundant collection of protein sequences from many different publicly accessible sources, including the UniProt Consortium databases Swiss-Prot, TrEMBL and PIR-PSD, translations from the EMBL/DDBJ/GenBank nucleotide sequence databases, the Protein Data Bank (PDB), NCBI's Reference Sequence Collection (RefSeq), and protein sequences from the European, American and Japanese Patent Offices.
UniProt/Swiss-Prot ID
UniProt/Swiss-Prot ID's come from the UniProt Knowledgebase, which was created by merging data in the Swiss-Prot, TrEMBL and PIR-PSD databases. The information in a UniProt/Swiss-Prot record is manually curated from computational analyses and literature.
UniProt/TrEMBL ID
UniProt/TrEMBL ID's come from the UniProt Knowledgebase, which was created by merging data in the Swiss-Prot, TrEMBL and PIR-PSD databases. The information in a UniProt/TrEMBL record is computationally generated and not manually curated.

If you know of other sequences for a particular locus that are not included on the appropriate "All Associated Sequences" page, please let us know by sending an email to yeast-curator@yeastgenome.org.

Associated Glossary Terms:

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