The following species databases are currently available for OligoWiz:
A. gambiae
A. nidulans
A. thaliana
B. subtilis
B. taurus (UniGene)
C. elegans
D. melanogaster
D. rerio
E. coli (K12)
G. Gallus (UniGene)
Human(UniGene)
Human genome
H. vulgare (UniGene)
L. lactis
M. loti
Mouse (UniGene)
Mouse genome
Nostoc sp. PCC7120
Rat (UniGene)
Rice (EST)
S. cerevisiae
S. pombe
S. scrofa (UniGene)
T. aestivum (UniGene)
The databases are used for both homology search and low-complexity detection. The databases are all based on collections of sequences originating from the indicated organisms. Two types of sequence collections are being used: one type is based on the full genome sequence and possible pladsmids commonly hosted by that organism, alternatively a UniGene database is used.
A. gambiae
The African malaria mosquito Anopheles gambiae database is based on the genbank entries NC_002084.1, NC_004818.1, NT_078267.2, NT_078268.1, NT_078266.1 and NT_078265.1
(downloaded 13th july 2004).
A. nidulans
The Aspergillus nidulans database is based on the aspergillus_nidulans_1.fasta.gz file found at Whitehead Institute Center for Genome Research (3th july 2003).
A. thaliana
The Arabidopsis thaliana database is based on the GenBank entries NC_003073, NC_003072, NC_003070, NC_003071, NC_003074, NC_001284, and NC_000932, representing the five chromosomes, the chloroplast and the mitochondria genomes of the A. thaliana (Columbia cultivar). (The Arabidopsis genome sequencing initiative)
B. subtilis
The Bacillus subtilis database is based on the GenBank entries NC_000964, NC_002075, NC_001765, NC_001764, and NC_001766, representing the B. subtilis genome, plasmid p1414, pTA1015, pTA1040 and pTA1060. (Kunst et al., Nature 390 (6657), 249-256 (1997))
B. taurus (UniGene)
The Bos taurus (Cattle) database is based on the UniGene collection (Bt.seq.uniq, Jul. 2003).
C. elegans
The Caenorhabditis elegans database is based on the GenBank entries NC_000965, NC_000966, NC_000967, NC_000968, NC_000969, NC_001130 and NC_001328, representing the C. elegans chromosomes and mitochondria genome.
(The C. elegans Sequencing Consortium, Science. 1998 Dec 11;282(5396):2012-8)
D. melanogaster
The Drosophila melanogaste database is based on the "large" and "small" scaffold collections (Science 287, 2185 (2000))
E. coli (K12)
The E. coli (K12) database is based on the GenBank entry U00096, representing the E. coli K-12 MG1655 chromosome.
(Blattner et al., Science 277 (5331), 1453-1474 (1997))
G. gallus (UniGene)
The chicken Gallus gallus database is based on the UniGene collection (Gga.seq.uniq, Juli 2004)
Human (UniGene)
The Homo sapiens database is based on the UniGene collection (Hs.seq.uniq, updated every second month)
Human genome
The Homo sapiens database is based on the Human genome.
Warning! Using this database is very time consuming; we recommend that you use the Human (UniGene) database, unless you have strong arguments for using the genome database.
!!! This database, has now been restricted to run on only 4 processors, due to server overload!!!
H. vulgare (UniGene)
The Hordeum vulgare or barley database is based on the UniGene collection (Hv.seq.uniq, Aug. 2003)
L. lactis
The Lactococcus lactis database is based on the GenBank entry NC_002662, representing the genome of L. lactis subsp. lactis. (IL140)
(Bolotin et al., Genome Res. 11 (5), 731-753 (2001))
M. loti
The Mesorhizobium loti database is based on the GenBank entry NC_002678.1, NC_002679.1 and NC_002682.1,
representing the genome, the plasmid pMLa and plasmid pMLb of M. loti respectively.
Mouse (UniGene)
The Mus musculus database is based on the UniGene collection (Mm.seq.uniq, Okt. 2003)
Mouse genome
The Mus musculus database is based on the Mouse genome
Warning! Using this database is very time consuming; we recommend that you use the Mouse (UniGene) database, unless you have strong arguments for using the genome database.
!!! This database, has now been restricted to run on only 4 processors, due to server overload!!!
Nostoc sp. PCC7120
The Nostoc sp. PCC7120 database is based on the GenBank entries NC_003272, NC_003240, NC_003267, NC_003273, NC_003270 and NC_003241.
Representing the Nostoc sp. PCC7120 genome, pCC7120beta, pCC7120gamma, pCC7120delta, pCC7120epsilon and pCC7120zeta respectively.
Rat (UniGene)
The Rattus norvegicus database is based on the UniGene collection (Rn.seq.uniq, Okt. 2003)
Rice (EST)
The Oryza sativa database is based on 207.504 rice EST sequences from both japonica and indica. The EST used sequences was downloaded from TIGR (updated 9.5.03 Rice.GB.EST.all.seq)
S. cerevisiae
The Saccharomyces cerevisiae database is based on the GenBank entries NC_001133, NC_001134, NC_001135, NC_001136, NC_001137, NC_001138, NC_001139, NC_001140, NC_001141, NC_001142, NC_001143, NC_001144, NC_001145, NC_001146, NC_001147 and NC_001148, representing the S. cerevisiae chromosomes and mitochondria genome. (Goffeau et al. Science 274 (5287), 546 (1996))
S. pombe
The Schizosaccharomyces pombe database is based on the GenBank entries NC_003424,NC_003423 NC_003421 NC_001326.1 representing the S. pombe chromosomes and mitochondria genome.
S. scrofa (UniGene)
The Sus scrofa or pig database is based on the UniGene collection (Ssc.seq.uniq, Okt. 2003)
T. aestivum (UniGene)
The Triticum aestivum or wheat database is based on the wheat UniGene collection (Ta.seq.uniq, Aug. 2003)
