Mammalian Homology to Yeast: Methods
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:
- Query Database: GenBank Protein datasets for human, mouse, rat, cow, and sheep
processed to remove duplicate sequences.
- Release date: 22 July 1997
- Software/Version: BLASTP 2.0a9MP-WashU [12-May-1997]
- Filters: xnu + seg
- Scoring matrix: BLOSUM62
- Gapping: Off
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 Unpublished;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:
- Software/Version: GCG gap program. 8.1-UNIX (osf), August 1995
- Gap creation penalty = 3.0
- Gap extension penalty = 0.1
- Scoring matrix: PAM250
OR
- Software/Version: GCG gap program. 9.0-UNIX (osf), December 1996
- Gap creation penalty = 12
- Gap extension penalty = 2
- Scoring matrix: BLOSUM62
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.
- Query Database: Non-redundant GenBank+EMBL+DDBJ+PDB
- Release date: October-November 1996
- GCG version: 8.1-UNIX (osf), August 1995
- Software/Version: TBLASTN 1.4.9MP (26-March-1996)
- Filters: xnu + seg
- Scoring matrix: BLOSUM62
Steve A. Chervitz and the SGD team
http://genome-www.stanford.edu/mammal/