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Sequence Set Browser

 

CAAM00000000.2 fossil metagenome

Master
# of Contigs: 64,265
# of Proteins: 0
Total length: 7,120,264 bp
BioProject: PRJNA17621
BioSample: SAMEA3138348
Keywords: WGS
Organism: fossil metagenomeshow lineagehide lineage
Biosource:
/country = Russia:Bol'shaya Kolopatkaya river
/environmental_sample
/isolation_source = Mammuthus primigenius fossil bone
/lat_lon = 70 N 151 E
/mol_type = genomic
WGS: CAAM02000001:CAAM02064265
Reference:
Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA : Proc. Natl. Acad. Sci. U.S.A. 103 (37), 13578-13584 (2006) – show 19 authorshide authors
Stiller,M., Green,R.E., Ronan,M., Simons,J.F., Du,L., He,W., Egholm,M., Rothberg,J.M., Keates,S.G., Ovodov,N.D., Antipina,E.E., Baryshnikov,G.F., Kuzmin,Y.V., Vasilevski,A.A., Wuenschell,G.E., Termini,J., Hofreiter,M., Jaenicke-Despres,V., Paabo,S.
Reference:
Patterns of damage in genomic DNA sequences from a Neandertal : Proc. Natl. Acad. Sci. U.S.A. 104 (37), 14616-14621 (2007) – show 11 authorshide authors
Briggs,A.W., Stenzel,U., Johnson,P.L.F., Green,R.E., Kelso,J., Pruefer,K., Meyer,M., Krause,J., Ronan,M.T., Lachmann,M., Paabo,S.
Submission:
Submitted (15-JUL-2006) Green R.E., Evolutionary Genetics, Max Planck Institute for Evol. Ant., Deutscher Platz 6, D-04103, GERMANY – Green,R.E.
Submission:
Submitted (29-MAY-2007) Green R.E., Evolutionary Genetics, Max Planck Institute for Evol. Ant., Deutscher Platz 6, D-04103, GERMANY – Green,R.E.

On Jul 3, 2007 this sequence version replaced gi:114049520.

The fossil metagenome whole genome shotgun (WGS) project has the project accession CAAM00000000. This version of the project (02) has the accession number CAAM02000000, and consists of sequences CAAM02000001-CAAM02064265.

Metagenomic set of sequence reads from DNA extract from 43,000 year-old mammoth bone from Bol'shaya Kolopatkaya river. Preliminary analysis found that 3% of these have their closest alignment to elephant, indicating that they are from the extinct mammoth. However, more are from prokaryotes that colonized the fossil later. These sequences use the same raw data as the previous CAAM/N-01 dataset, processed according to an updated pipeline (runNeandertalPipe) specially tailored to ancient DNA. The pipeline involves leaving 454 adaptors and other normally trimmed sequence in the final FASTA sequences, allowing precise identification of the ends of the ancient sequences.

Contigs
Download
GenBank:CAAM02.1.gbff.gz 6.5 Mb
FASTA:CAAM02.1.fsa_nt.gz 2.6 Mb
ASN.1:CAAM02.1.bbs.gz 3.7 Mb