Table 1

Runtime comparison for five small genomes between HMMER, RPS-BLAST, UFO and batch search at the Pfam web site (March 2009).

CPU time

Species

# Proteins

HMMER

RPS-BLAST

Pfam-web

UFO

A. pseudotrichon.

847

19 h 37 m

4 m 11 s

9 h 28 m

2.5 s

E. chaffeensis

803

17 h 58 m

3 m 13 s

9 h 19 m

2.0 s

U. parvum

577

13 h 54 m

3 m 46 s

7 h 38 m

1.8 s

U. urealyticum

611

14 h 36 m

3 m 42 s

8 h 03 m

1.9 s

W. endosymbiont

746

16 h 49 m

3 m 40 s

8 h 42 m

1.9 s

Meinicke BMC Genomics 2009 10:409   doi:10.1186/1471-2164-10-409