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Eukaryotic Organism Databases
(Genome Assemblies, ESTs etc.)

Human databases

Golden Path Human Genome Assembly, May, 2004 (hg17)
Description

The latest assembly of human genome.
Date
May, 2004

Every chromosome is represented in a separate database.
The sequence data could be masked for repeats and split into fragments by 100K with 10K overlap. Thus, four types of representation exist:

  1. unsplit and unmasked
  2. unsplit and masked
  3. 100K split and unmasked
  4. 100K split and masked

However, due to space limitations, currently only the split, unmasked copy is available except by special request.

Location on BLASTER.
 genomes/human/goldenPath_May2004/100

To search the whole genome on BLASTER using command line type the database directory with star as database. For example:
>pb blastall -d genomes/human/goldenPath_May2004/100/* [other options]

To learn more about BLASTER usage please consult the manual.
Location on GeneMatcher.
 /fdf/genematcher/gm0/0/genomes/human/goldenPath_May2004/100
Each chromosome is arranged into separate database on GENEMATCHER. Whole genome arrangted as dataset, which inculde all chromosomal databases. The datasets are:


goldenPath_May2004_100
goldenPath_May2004_100.codon
goldenPath_May2004_100.rframe

Important note: rarely used representations and databases could be temporary removed from GENEMATCHER. Contact our personell if you don't see required data on GENEMATCHER.

To learn more about using GENEMATCHER usage please consult the manual.

 

 

EST_HUMAN
Description

Human subset of GenBank+EMBL+DDBJ sequences from NCBI EST Division
Updates
Weekly or more.
Location on BLASTER.
 db1/ncbi/est_human
or
db2/ncbi/est_human
Location on GeneMatcher.
 /fdf/genematcher/gm0/1/ncbi/est_human
notes
  

Mouse

Golden Path Mouse Genome Assembly, February 2003 (mm3)
Description

The latest assembly of mouse genome.
Date
Date of assembly release February, 2003
Date of last revision May, 2003.

Every chromosome is represented in a separate database.
The sequence data presented as:

  1. unsplitted and unmasked
  2. 100K split and unmasked

Each representation located in separate directory.
Location on BLASTER.

Unsplit data:
genomes/mouse/goldenPath_Feb2003/
Splite data:
genomes/mouse/goldenPath_Feb2003/100

To search the whole genome on BLASTER using command line type the database directory with star as database. For example:

>pb blastall -d genomes/mouse/goldenPath_Feb2003/100/* [other options]

To learn more about BLASTER usage please consult the manual.
Location on GeneMatcher.
 Unsplit data:
/fdf/genematcher/gm0/0/genomes/mouse/goldenPath_Feb2003/
Split data:
/fdf/genematcher/gm0/0/genomes/mouse/goldenPath_Feb2003/100
Each chromosome is arranged into separate database on GENEMATCHER. Whole genome arrangted as dataset, which inculde all chromosomal databases. The datasets are:

mouse_gp_Feb2003
mouse_gp_Feb2003.codon
mouse_gp_Feb2003.rframe
mouse_gp_Feb2003_100
mouse_gp_Feb2003_100.codon
mouse_gp_Feb2003_100.rframe

Important note: rarely used representations and databases could be temporary removed from GENEMATCHER. Contact our personell if you don't see required data on GENEMATCHER.

To learn more about using GENEMATCHER usage please consult the manual.

 

EST_MOUSE
Description

Mouse subset of GenBank+EMBL+DDBJ sequences from NCBI EST Division
Updates
Weekly or more.
Location on BLASTER.
 db1/ncbi/est_mouse
or
db2/ncbi/est_mouse
Location on GeneMatcher.
 /fdf/genematcher/gm0/1/ncbi/est_mouse
notes
  

Rat

Not yet installed.

Zebra Fish

Not yet installed.

Fugu

JGI Fugu Genome Assembly (v3.0)
Description

The latest assembly of fugu fish genome.
Besides nucleotide data the fugu proteom is represented.
Date
26 August 2002
Location on BLASTER.
 genome assembly:
genomes/fugu/dgifugu_v3_Aug2002
proteome:
genomes/fugu/dgifugu_v3_prot_Aug2002
Location on GeneMatcher.
 /fdf/genematcher/gm0/0/genomes/fugu/fugu_v3_Aug2002.codon
/fdf/genematcher/gm0/0/genomes/fugu/fugu_v3_Aug2002.dna
/fdf/genematcher/gm0/0/genomes/fugu/fugu_v3_Aug2002.rframe
/fdf/genematcher/gm0/0/genomes/fugu/fugu_v3_prot_Aug2002.prot

GENEMATCHER datasets are:

fugu
fugu.codon
fugu.prot
fugu.rframe

Ciona

Ciona savignyi Genome Assembly (v3.0)
Description

The assembly of Ciona savignyi (sea squirt) genome by Whitehead Institute Center for Genomic Research.
Besides genomeic nucleotide data the mRNA sequences (transcriptom) are avaliable.
Date
August 20 2001
Location on BLASTER.
 genomes/ciona/
Location on GeneMatcher.
 /fdf/genematcher/gm0/0/genomes/ciona/

GENEMATCHER datasets are:

ciona
ciona.masked
ciona_mrna

Drosophila

Drosophila melanogaster genome assembly (Release 3.1)
Description
The sequence Drosophila melanogaster genome, originally determined in a collaboration between Celera and the Berkeley Drosophila Genome Project, is described in the March 24, 2000 issue of Science. More recently, the Berkeley Drosophila Genome Project has corrected and expanded the sequence (Celniker et al., 2002), and the FlyBase Consortium has re-annotated this improved sequence (Misra et al., 2002).
Date
Last update was February, 2003
Location on BLASTER.

db1/ncbi/
or
db2/ncbi/
Location on GeneMatcher.
 /fdf/genematcher/gm0/1/ncbi/

GENEMATCHER datasets are:

drosophila
ciona.masked
ciona_mrna

Anopheles

Under construction.

C. elegans

Caenorhabditis elegans Genome Assembly
Description

The latest assembly of C.elegans genome by Sanger Center and the Genome Sequencing Center at the Washington University. The genome is 97Mb, organized in 6 chromosomes. Each chromosome formatted as a separate database.
Date
Project finished in 1998, sporadic updates since then.
Location on BLASTER.
 genome assembly:
genomes/fugu/dgifugu_v3_Aug2002
proteome:
genomes/fugu/dgifugu_v3_prot_Aug2002
Location on GeneMatcher.
 /fdf/genematcher/gm0/0/genomes/c_elegans

GENEMATCHER datasets are:

c_elegans
c_elegans.codon
c_elegans.rframe

Yeast

Under construction.
 
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