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NCBI Trace Archive specifications

Information


Unique identifier OMICS_05337
Name NCBI Trace Archive
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Eric W Sayers

Publication for NCBI Trace Archive

NCBI Trace Archive citations

 (50)
library_books

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

2017
PLoS Biol
PMCID: 5531438
PMID: 28749982
DOI: 10.1371/journal.pbio.2002266

[…] spinulosus were downloaded from the NCBI Transcriptome Shotgun Assembly (TSA) Database. EST sequences of Euperipatoides kanangrensis, Peripatopsis sedgwicki, and Echinoderes horni were download from NCBI Trace Archive and assembled using CAP3 []. Raw mRNA-Seq reads for Peripatopsis capensis were downloaded from NCBI SRA, trimmed using skewer [], and assembled with Trinity []. Protein sequences we […]

library_books

The Plasmodium PHIST and RESA Like Protein Families of Human and Rodent Malaria Parasites

2016
PLoS One
PMCID: 4811531
PMID: 27022937
DOI: 10.1371/journal.pone.0152510

[…] isolate nucleotide sequence databases (HB3, Dd2, RO-33/Ghana, D6, D10, VS/1, K1/Thailand, Santa Lucia, FCC-2/Hainan and Senegal V34.04; Broad Institute; downloaded for local TBLASTN analyses from the NCBI Trace Archive; as well as SNP data from the MalariaGen Pf3k project, www.malariagen.net/apps/Pf3k) indicates that the orthologous members from each isolate are 99–100% conserved (data not shown; […]

library_books

High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events

2016
Front Plant Sci
PMCID: 4806543
PMID: 27047500
DOI: 10.3389/fpls.2016.00308

[…] en DNA from CentC-containing colonies were Sanger sequenced at Pacific Biosciences Research Center Biotech Core (Honolulu, HI, USA) using vector primers SL1 and NZRevC. Sanger sequences (available at NCBI Trace Archive TI numbers 2343263554-2343263871) were assembled in Consed (Gordon et al., ) where discrepancies between assembled reads were manually edited before generating a consensus sequence. […]

call_split

Host Mitochondrial Association Evolved in the Human Parasite Toxoplasma gondii via Neofunctionalization of a Gene Duplicate

2016
Genetics
PMCID: 4858780
PMID: 26920761
DOI: 10.1534/genetics.115.186270
call_split See protocol

[…] Copy number analysis was performed as described previously (; ). Briefly, raw sequence reads from multiple T. gondii strains and N. caninum (Liverpool strain) () were downloaded from the NCBI trace archive in fasta format (strains GT1, ME49, and VEG were derived from Sanger-based shotgun sequencing; MAS, P89, FOU, VAND, and RUB were generated using Roche 454 technology). T. gondii and […]

library_books

Expression of a Novel D4 Dopamine Receptor in the Lamprey Brain. Evolutionary Considerations about Dopamine Receptors

2016
Front Neuroanat
PMCID: 4701969
PMID: 26778974
DOI: 10.3389/fnana.2015.00165

[…] egion was also retrieved from the Ensembl project server (Ensembl Protein: ENSPMAP00000010574).In order to retrieve the final portion of the protein, additional searches were carried out by using the NCBI trace archive databases. Although some additional fragments corresponding to the end of the D4 sequence were obtained, they did not overlap with the final part of the sequence obtained from the U […]

library_books

The Rickettsia Endosymbiont of Ixodes pacificus Contains All the Genes of De Novo Folate Biosynthesis

2015
PLoS One
PMCID: 4674097
PMID: 26650541
DOI: 10.1371/journal.pone.0144552

[…] Our findings that R. buchneri in I. scapularis has all five genes required for the synthesis of folate were based on MUMmer alignments and MetaCyc metabolic reconstructions using the NCBI Trace Archive data from the I. scapularis genome sequencing project [, ]. The bioinformatics analyses were carried out before the complete annotation of the genome of I. scapularis was released i […]

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