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Sequence Set Browser


GABC00000000.1 Pan troglodytes

# of Contigs: 29,054
# of Proteins: 10,874
Total length: 55,417,641 bp
BioProject: PRJNA173089
Sequence Read Archive: SRR544868
Keywords: TSA
Annotation: Contigs
Organism: Pan troglodytesshow lineagehide lineage
/cell_line = untransformed stem cells
/isolation_source = Clint
/mol_type = mRNA
/tissue_type = adipose stromal
WGS: GABC01000001:GABC01029054
De novo assembly of the reference chimpanzee transcriptome from NextGen mRNA sequences : Unpublished – Maudhoo,M.D., Meehan,D.T., Norgren,R.B. Jr.
Submitted (15-OCT-2012) Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA – Maudhoo,M.D., Meehan,D.T., Norgren,R.B. Jr.

Paired-end, 101 bp sequencing was performed on the Illumina platform. All reads were aligned with the human RefSeq mRNA transcripts using BLAST. Any reads with an alignment length difference with respect to the human reference sequence of 2 or greater were removed prior to assembly. For a given pair of reads, if one sequence was filtered, its pair was also filtered. Velveth was performed as recommended. kmer was set at 31. The output files from Velveth were passed to Velvetg. After performing Velvetg, this output file was passed to Oases where the final assembly was performed. Default parameters were used for Velvetg and Oases.

Assembly Method : Velvet 1.2.07; Oases 0.2.08
Sequencing Technology : Illumina HiSeq
GenBank:GABC01.1.gbff.gz 25.7 Mb
FASTA:GABC01.1.fsa_nt.gz 13.3 Mb
ASN.1:GABC01.1.bbs.gz 16.5 Mb