SGD

Mammalian Homology to Yeast: Methods

Mammalian Vertebrate Methods XREFdb

Yeast-vs-Mammal BLASTs:

This site serves up pre-existing BLAST reports between each S. cerevisiae open reading frame (ORF) peptide sequence in SGD and all unique protein sequences in the human, mouse, rat, cow, and sheep sequences in GenBank.

Technical details:

Reference:Gish, Warren (1994-1997). Unpublished; Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). J. Mol. Biol. 215:403-10.

Needleman-Wunsch Alignments:

OR

Reference: Needleman, S.B. and Wunsch, C.D. (1970). J. Mol. Biol. 48:443-453.

Yeast-vs-Vertebrate BLASTs:

The data in the homolog summary table was obtained by BLASTing each S. cerevisiae open reading frame (ORF) peptide sequence in SGD against translations of all nucleotide sequences in the non-redundant collection of GenBank, EMBL, DDBJ, and PDB databases. All database sequences producing P-values of 1e-10 or lower and classified as Primate, Rodent, Other mammalian, or Other vertebrate by GenBank were then tallied for each yeast ORF.


Steve A. Chervitz and the SGD team
http://genome-www.stanford.edu/mammal/