TABLE 1.

Similarity searches^a

Target				Method	Query (GSS data set)	Result of query
Database or sequence	Date posted	No. of sequences	No. of letters
GenBank Alveolata	8 August 2000	36,628	29,939,175	BLASTN 2.0.14	hq	3 rRNA genes; 6 protein coding genes
Swall				BLASTX 2.0.12	nr	722 ORFs
Swissprot	7 July 2000	86,593	31,411,157
Swissprotnew	8 July 2000	2,822	1,280,954
Sptrembl	28 June 2000	297,973	93,374,136
Sptrnew	8 July 2000	71,201	22,367,698
Pfam	21 September 2000	111,934	38,089,901	BLASTP 2.0.14	ORF	524 PfamA domains
Proteome				BLASTP 2.0.14	ORF
E. coli	4 January 2001	4,581	1,435,304			101 hitsb
S. cerevisiae	15 November 2000	6,358	2,991,939			505 hitsb
C. elegans	15 November 2000	19,704	8,596,400			586 hitsb
D. melanogaster	15 November 2000	14,080	6,850,524			599 hitsb
A. thaliana	6 January 2001	25,458	11,049,032			588 hitsb
H. sapiens	15 November 2000	31,919	13,433,624			616 hitsb
hq	2 November 2000	3,046	1,403,056	TBLASTX 2.0.14	hq	108 families

^aThe genome survey sequence (GSS) data set used for each query is as follows: nr, nonredundant data (3,139 reads; 3,481,394 nt); hq, high-quality nonredundant data (3,046 reads, 1,403,056 nt); and ORF, set of 722 ORF fragments identified by similarity (107,303 aa).

^bThreshold, E < 10⁻⁴.