TJGR
things just got real
Zhang, G; Fang, X; Guo, X; Li, L; Luo, R; Xu, F; Yang, P; Zhang, L; Wang, X; Qi, H; Zhu, Y; Yang, L; Huang, Z (2012) Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030
Other Resources: OysterDB (Blast, Downloads) | Related manuscript: doi:10.1038/nature11413
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[ http://genefish.wikispaces.com/page/xml/crassostreome?v=rss_2_0]
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oyster.v9_M
Sequence
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FASTA
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60 Sequences; 75 MB
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BSMAP
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SAM
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BS MBD
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RNAseq
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SAM
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PROPS: DH
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RNAseq
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SAM
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PROPS: BBC
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RefMap
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SAM
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MBD Library
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Annotation
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BED
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BS MBD CG features (no scores)
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Annotation
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BED
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BS MBD CG features (with scores)
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Annotation
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BED
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BS MBD CG features (0-20%)
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Annotation
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BED
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BS MBD CG features (20-70%)
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Annotation
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BED
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BS MBD CG features (70-100%)
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Annotation
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GFF
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Tandem Repeats [Phobos] (imperfect search)
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Annotation
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BED
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Tandem Repeats (interval and ID only)
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Annotation
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BED
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Complement to CDS features
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Annotation
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GFF
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CG motifs
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Annotation
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GFF
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CG motifs non overlap w BS MBD CG (~250k)
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Annotation
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GFF
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CG motifs with methylation status (~500k)
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Annotation
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BED
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CG motifs(~500k) (interval and ID only)
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Annotation
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BED
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50bp region (up and down) flanking CG motifs(~500k)
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Sequence
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FASTA
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50bp region (up and down) flanking CG motifs(~500k)
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Annotation
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GFF
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CG motifs (of 500k) that overlap with Tandem Repeats
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Annotation
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Blast Table
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Transposable Elements: RepBase inv Blast
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Annotation
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BED
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Transposable Elements: evalue 1E-10
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Annotation
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BED
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Transposable Elements: evalue 1E-10; single directionality
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Data
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Tab Text
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Interval Join: CG motifs(~500k) and TEs (RepBase)
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Data
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Tab Text
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Interval Join: CG motifs(~500k) and Repeats (Phobos)
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Data
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Tab Text
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Interval Join: CG motifs(~500k) and exons (CDS)
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Data
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Tab Text
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Interval Join: CG motifs(~500k) and closest non overlapping exons
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Data
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Tab Text
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Interval Join: CG motifs(~500k) not overlapping w/ mRNA (extragenic)
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Description: Genomic scaffolds longer that 1M bps
oyster.v9_90
Sequence
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FASTA
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1670 Sequences; 488 MB
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Annotation
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Tab Text
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Tiling Array Design v1
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Description: Longest genomic scaffolds (1670; 14%) that cover over 90% of genome.
oyster.v9_proteome
Sequence
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FASTA
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[.gz] 28027 protein sequences (via gigadb.org)
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Sequence
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FASTA
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28027 protein sequences (local)
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Annotation
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Blast Table
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Blastp Swiss-Prot evalue: 10
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Annotation
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Blast Table
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Blastp Swiss-Prot evalue: 1E-05
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Annotation
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Blast Table
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Blastp Estrogen Biosynthetic Process; 1E-20, 4 max_targets, (details)
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Description: Proteins
oyster.v9_genes
Sequence
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FASTA
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[.gz] 28027 gene (CDS only) sequences (via gigadb.org)
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Sequence
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FASTA
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28027 gene (CDS only) sequences (local)
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Annotation
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Blast table
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Blastx Swiss-Prot evalue: 1E-05
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Data
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Tab Text
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Number of exons per gene
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Annotation
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Tab Text
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Corresponding SPID and evalues
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Annotation
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Tab Text
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Corresponding SPID, evalues, and descriptions
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Annotation
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Tab Text
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Corresponding SPID, evalues, and GO# (using recent GO file)
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Annotation
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Tab Text
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Corresponding SPID, evalues, and GO and GOslim
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Description: Coding sequence
oyster.v9
Sequence
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FASTA
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[.gz] 11969 Sequences (via gigadb.org)
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Sequence
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FASTA
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[.gz] 11969 Sequences (local)
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Sequence
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FASTA
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11969 Sequences (local) 560MB
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Annotation
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GFF
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[.gz] gene features (via gigadb.org)
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Annotation
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GFF
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gene features (CDS and mRNA)
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Annotation
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GFF
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gene features (CDS only)
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Annotation
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BED
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gene features (CDS only) (interval and ID)
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Annotation
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GFF
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gene features (mRNA only)
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Annotation
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BED
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gene features (mRNA only)
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Annotation
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GFF
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promoter region (1000bp 5' of mRNA)
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Annotation
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GFF
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mRNA GOslim = cell adhesion or signal transduction or cell-cell signaling
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Annotation
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GFF
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mRNA GOslim = DNA metabolism or RNA metabolism or protein metabolism
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Annotation
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GFF
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DESeq (p<0.05) Gill v Male Gonad RNA-seq from Zhang et al
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Description: Zhang, G; Fang, X; Guo, X; Li, L; Luo, R; Xu, F; Yang, P; Zhang, L; Wang, X; Qi, H; Zhu, Y; Yang, L; Huang, Z (2012) Genomic data from the Pacific oyster (
Crassostrea gigas). GigaScience.
http://dx.doi.org/10.5524/100030
TGAGA (alpha)
towards getting a gigas assembly (alpha)
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cgigas_alpha_v0.4.0
Sequence
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FASTA
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230,270 Sequences
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Description: Independent assembly of 19 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset.
Combination of assemblies v0.2.0 and v0.3.1.
cgigas_alpha_v0.3.2
Description: Independent assembly of 10 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset. Sequences greater than 20k bp retained. Cgigas BAC clones from NCBI (60) reduced to 53 clusters. Plus 12 select sequences with known genomic structure.
cgigas_alpha_v0.3.1
Sequence
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FASTA
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500MB
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203,216 Sequences
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Description: Independent assembly of 10 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset.
cgigas_alpha_v0.3.0
Description: Independent assembly of 10 fosmids. Consensus sequences >20,000bp along with publicly available BAC sequences were analyzed using CD-HIT EST to obtain non-redundant dataset. Plus 12 select sequences with known genomic structure.
cgigas_alpha_v0.2.0
Sequence
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FASTA
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615MB
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205,903 Sequences
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Annotation
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Description: Independent assembly of nine fosmids. Consensus sequences were analyzed using CD-HIT EST to obtain non-redundant dataset.
cgigas_alpha_v0.1.3
Sequence
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FASTA
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6MB
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262 Sequences
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Annotation
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Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset. Remaining sequences greater than 20,000 bp are included. Plus 12 select sequences with known genomic structure.
cgigas_alpha_v0.1.2
Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset. Plus 12 select sequences with known genomic structure.
cgigas_alpha_v0.1.1
Sequence
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FASTA
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215MB
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28,526 Sequences
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Annotation
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Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset.
cgigas_alpha_v0.1.0
Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset. Remaining sequences greater than 20,000 bp are included.
cgigas_PREalpha_v0.2.0
*
BLAST option: blastn,
megablast select database from menu
Related Resources
various other genomic resources for the oyster.
GigasBase
The Oyster EST contig browser aims to produce and maintain an automatic annotation of Oyster EST libraries. This database
GigasDatabase was initiated within the frame of the
AquaFirst European project, it now gathers EST sequences produced by a
Marine Genomics Europe project (GOCE-CT-2004-505403) and a
Genoscope project.
GigasDatabase is regularly updated in the context of the ANR project "Gametogenes" (ANR-08-GENM-041).
GigasDatabase Assemblies
Version 8
cgigas_all_contigs_v8.fa
cgigas_all_contigs_v8_BESTHIT.tsv
cgigas_all_contigs_v8_ontology.tsv
Archived GigasDatabase Assemblies
Version 6
Sigenae_v6_assembly.fa
Sigenae _v6_SPhits.xls
NCBI
Crassostrea gigas Entrez Records
Crassostrea virginica Entrez Records
NCBI: SRA
Crassostrea gigas
FASTA export of quality trimmed reads (export date 02/10/11)
Misc
Cgigas_BAConly.fa (export date 01/31/11)
Cgigas_genomic_NCBI.fa (export date 01/31/11)
Roberts Lab Submissions
Crassostrea Nucleotide Database entries
Crassostrea gigas EST Database entries
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