Shown are the directory paths and
filenames of sequence files on the BlastMachine and
UNIX fileserver. On the GeneMatcher2, the same basic
directory structure is present, but to refer to individual
files the entire path from the root must be specified.
Shortcuts called dbsets can be used on the GeneMatcher2.
See details on GeneMatcher2 file locations and dbsets
here.
Anopheles
genomes/anopheles/unsplit/
anopheles_cdna
anopheles_cdna_known
anopheles_cdna_novel
anopheles_contig
anopheles_contig_masked
anopheles_pep
anopheles_pep_known
anopheles_pep_novel
genomes/anopheles/100/
anopheles_cdna
anopheles_cdna_known
anopheles_cdna_novel
anopheles_contig
anopheles_contig_masked
Bacterial
genomes/bacterial/
AeropyrumPernix
AgrobacteriumTumefaciensC58
AquifexAeolicus
BacillusHalodurans
BacillusSubtilis
BrucellaMelitensis
BuchneraSp
CampylobacterJejuni
CaulobacterCrescentus
ChlamydiaMuridarum
ChlamydiaPneumoniae
ChlamydiaPneumoniaeGWL029
ChlamydiaTrachomatis
ChlamydiophilaPneumoniaeJ138
ChlamydophilaPneumoniaeAR39
ClostridiumAcetobutylicum
ClostridiumPerfringens
DeinococcusRadiodurans
FusobacteriumNucleatum
LactococcusLactis
ListeriaInnocua
ListeriaMonocytogenes
MesorhizobiumLoti
MethanobacteriumThermoautotrophicum
MethanopyrusKandleri
MethanosarcinaAcetivorans
MycobacteriumLeprae
MycoplasmaPneumoniae
MycoplasmaPulmonis
NeisseriaMeningitidis
PasteurellaMultocida
PseudomonasAeruginosas
PyrobaculumAerophilum
PyrococcusAbyssi
PyrococcusFuriosus
PyrococcusHorikoshii
RickettsiaConorii
RickettsiaProwazekii
SalmonellaTyphimurium
StaphylococcusAureus
StreptococcusPneumoniae
StreptococcusPyogenes
SulfolobusSolfataricus
SulfolobusTokodaii
SynechocystisPCC6803
ThermoanaerobacterTengcongensis
ThermoplasmaAcidophilum
ThermoplasmaVolcanium
UreaplasmaUrealyticum
VibrioCholerae
XylellaFastidiosa
Ciona
intestinalis (sea squirt)
genomes/ciona/
cionaV1 (unmasked genome)
cionaV1_masked (masked genome)
cionaV1mrna
cionaV1prot
C. elegans
genomes/c_elegans/
ce_i
ce_ii
ce_iii
ce_iv
ce_v
ce_x
Drosophila
genomes/drosophila/
drosophila.aa
drosophila.nt
Fugu
genomes/fugu/dgi/
fugu_assembly
fugu_v3_Aug2002
fugu_v3_prot_Aug2002
Human Repeats
genomes/human/
HumanRepeats
Human - Golden Path Genome
Assembly of May 2004 (hg17, with chromosomes split
into 100K pieces with 10K overlap)
genomes/human/goldenPath_May2004/100/
chr1.fa
chr2.fa
chr2_random.fa
chr3.fa
chr3_random.fa
chr4.fa
chr4_random.fa
chr5.fa
chr5_random.fa
chr6.fa
chr6_random.fa
chr7.fa
chr7_random.fa
chr8.fa
chr8_random.fa
chr9.fa
chr9_random.fa
chr10.fa
chr10_random.fa
chr11.fa
chr12.fa
chr12_random.fa
chr13.fa
chr13_random.fa
chr14.fa
chr15.fa
chr15_random.fa
chr16.fa
chr16_random.fa
chr17.fa
chr17_random.fa
chr18.fa
chr18_random.fa
chr19.fa
chr19_random.fa
chr20.fa
chr21.fa
chr22.fa
chr22_random.fa
chrX.fa
chrX_random.fa
chrY.fa
Note - the masked version is available on request.
Mouse - ensembl assembly April
2002
genomes/mouse/ensembl/
MGSC_2002April11_V3
Mouse - Golden Path Genome
Assembly of February 2003 (mm3, with chromosomes not
split)
genomes/mouse/goldenPath_Feb2003/unsplit/
chr4_random
chr5
chr5_random
chr6
chr6_random
chr7
chr7_random
chr8
chr8_random
chr9
chr9_random
chr10
chr11
chr12
chr12_random
chr13
chr13_random
chr14
chr14_random
chr15
chr16
chr17
chr17_random
chr18
chr18_random
chr19
chrUn_random
chrX
chrX_random
chrY_random
Mouse - Golden Path Genome
Assembly of February 2003 (mm3, with chromosomes split
into 100K pieces with 10K overlap)
genomes/mouse/goldenPath_Feb2003/100/
chr1
chr1_random
chr2
chr2_random
chr3
chr3_random
chr4
chr4_random
chr5
chr5_random
chr6
chr6_random
chr7
chr7_random
chr8
chr8_random
chr9
chr9_random
chr10
chr11
chr12
chr12_random
chr13
chr13_random
chr14
chr14_random
chr15
chr16
chr17
chr17_random
chr18
chr18_random
chr19
chrUn_random
chrX
chrX_random
chrY_random
Rat - GoldenPath Genome Assembly
of June 2003 (rn3)
genomes/rat/
chr1
chr1_random
chr2
chr2_random
chr3
chr3_random
chr4
chr4_random
chr5
chr5_random
chr6
chr6_random
chr7
chr7_random
chr8
chr8_random
chr9
chr9_random
chr10
chr10_random
chr11
chr11_random
chr12
chr12_random
chr13
chr13_random
chr14
chr14_random
chr15
chr15_random
chr16
chr16_random
chr17
chr17_random
chr18
chr18_random
chr19
chr19_random
chr20
chr20_random
chrUn
chrUn_random
chrX
chrX_random
Tetraodon - May 2002
genomes/tetraodon/2002_May/
tr
Tetraodon - Reads
genomes/tetraodon/reads/
tr
Yeast
genomes/yeast/
yeast.aa
yeast.nt
Zebra Fish
genomes/zebra_fish/unsplit/
zebra_fish_cdna_genscan
zebra_fish_cdna_known
zebra_fish_cdna_novel
zebra_fish_contig
zebra_fish_contig_masked
zebra_fish_pep
zebra_fish_pep_genscan
zebra_fish_pep_known
zebra_fish_pep_novel
genomes/zebra_fish/100/
zebra_fish_cdna_genscan
zebra_fish_cdna_known
zebra_fish_cdna_novel
zebra_fish_contig
zebra_fish_contig_masked
