Notes on methods used in Chervitz et al., XXXXX, Science, XXXXX
(1998)
The dataset used for these comparisons was the October 16, 1998 worm
protein dataset from the Sanger Institute and the ORF translations in the
October 28 version of the Saccharomyces Genome Database (both are
available from the Science website as well as SGD). Because the
prediction of C. elegans protein sequences had, on October 16th, yet
to be corrected by rigorous experimental analysis, our reliance on
these predictions may result in the loss of some subset of C. elegans
proteins. However using the subset of yeast proteins for which we had
identified no worm homolog we performed BLAST searches against 6 frame
translations of the entire worm DNA sequence (finished sequence from
the Sanger Institute website as of Nov. 3, 1998), and identified no
additional homologs at the P<10-10 level with the >80% alignment
requirement (JMC unpublished).
References for BLAST versions that were used
S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman, J.
Mol. Biol. 215, 403 (1990).; W. Gish and D. J. States, Nature Genetics
3, 266 (1993); S. Karlin and S. F. Altschul. Proc. Natl. Acad. Sci.
90, 5873 (1993); S. F. Altschul and W. Gish Methods in Enzymology 266,
460 (1996). Version 2.0a19MP-WashU of BLAST was used, utilizing the
XNU and SEG filters, BLOSUM62 scoring matrix, with gapping on, and
other parameters set to default values.
