The ORFanage: An ORFan database

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Siew, Naomi ^a   Azaria, Yaniv ^a   Fischer, Daniel ^a,b  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BACILLUS; BACILLUS SUBTILIS; CELL LINEAGE; CONTROLLED STUDY; EVOLUTION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENETIC DATABASE; INTERNET; MICROBIAL GENETICS; MULTIGENE FAMILY; NONHUMAN; OPEN READING FRAME; ORFANAGE DATABASE; PARALOGY; PREDICTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENES, BACTERIAL; INTERNET; OPEN READING FRAMES; SEQUENCE HOMOLOGY; SPECIES SPECIFICITY;

BACILLUS SUBTILIS; POSIBACTERIA;

EID: 0346494928     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (16)

1. Siew,N. and Fischer,D. (2003) Twenty thousand ORFan microbial protein families for the biologist? Structure, 11, 7-9.
2. Siew,N. and Fischer,D. (2003) Unraveling the ORFan puzzle. Comp. Funct. Genomics, 4, 432-441.
3. Kunin,V., Cases,I., Enright,A.J., de Lorenzo,V. and Ouzounis,C.A. (2003) Myriads of protein families and still counting. Genome Biol., 4, 401-402.
4. Fischer,D. and Eisenberg,D. (1999) Finding families for genomic ORFans. Bioinformatics, 15, 759-762.
5. Fischer,D. (1999) Rational structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Protein Eng., 12, 1029-1030.
6. Siew,N. and Fischer,D. (2003). Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins, 52, 241-251.
7. Gardner,M.J., Hall,N., Fung E., White,O., Berriman,M., Hyman,R.W., Carlton,J.M., Pain,A., Nelson,K.E., Bowman,S. et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419, 498-511.
8. Boucher,Y., Nesbo,C.L. and Doolittle,W.F. (2001) Microbial genomes: dealing with diversity. Curr. Opin. Microbiol., 4, 285-289.
9. Dujon,B. (1996) The Yeast Genome Project: what did we learn? Trends Genet., 12, 263-270.
10. Tatusov,R.L., Galperin,M.Y., Natale D. A. and Koonin,E.V. (2001) The COG Database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
11. Andrade,M.A., Daruvar,A., Casari,G., Schneider,R., Termier,M. and Sander,C. (1997) Characterization of new proteins found by analysis of short open reading frames from the full yeast genome. Yeast, 13, 1363-1374
12. Skovgaard,M., Jensen,L.J., Brunak,S., Ussery,D. and Krogh A. (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends Genet., 17, 425-428.
13. Mackiewicz,P., Kowalczuk,M., Gierlik,A., Dudek,M. and Cebrat,S. (1999) Origin and properties of non-coding ORFs in the yeast genome. Nucleic Acids Res., 27, 3503-3509.
14. Basrai,M.A., Hieter,P. and Boeke,J.D. (1997) Small open reading frames: beautiful needles in the haystack. Genome Res., 7, 768-771.
15. Ochman,H. (1996) Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet., 18, 325-327.
16. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.