The GenBank genetic sequence databank

Bilofsky, Howard S.; Burks, Christian; Fickett, James W.; Goad, Walter B.; Lewitter, Fran; Rindone, Wayne P.; Swindell, C. D.; Tung, Chang‐Shung

doi:10.1093/nar/14.1.1

Cited by 337 publications

(77 citation statements)

References 2 publications

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“…However, it is well known that many repeated sequences, such as moderately repetitive DNAs, highly repetitive DNAs, RNA genes (rRNA, tRNA), satellite DNA, histone gene and a large amount of poly A sequences, constitute over 50 ~ of human genome (Britten and Davidson, 1971 ;Darnell, 1976Darnell, , 1983Pardue and Gall, 1970;Singer and Skowronski, 1985;Sinclair and Brown, 1971;Jelinek and Schmid, 1982). For example, repeated sequences with four identical nucleotides (AAAA or GGGG or CCCC or TTTT) can be matched 9.1 x 105 times in the total DNA sequence (8.3 x 107 bases) entered in GenBank (see Release 71.0 of GenBank, Bilofsky et al, 1986). There is no doubt that the more identical nucleotides are repeated within a sequence, the more matches there will be between this sequence and human genomic DNA.…”

Section: Resultsmentioning

confidence: 99%

A mathematically designed STS primer without any mismatches for direct sequencing of cosmid DNA clones

et al. 1993

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SummaryWe report here a new method for the direct sequencing of large DNA inserts of cosmid clones from human chromosomes using STS primers of 14 nucleotides without any mismatches, which are designed from results of a mathematical analysis. It is clear that STS primer of 14 nucleotides is optimum for direct sequencing of cosmid recombinant DNA clones. We also provide examples of direct sequencing of cosmid clones of human chromosome 21 using these STS primers.

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Section: Resultsmentioning

confidence: 99%

A mathematically designed STS primer without any mismatches for direct sequencing of cosmid DNA clones

et al. 1993

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“…There is a single consensus site for N-linked glycosylation at Asn-41. Comparison ofthe cDNA sequence to the GenBank data base (20) suggests that the SR13 mRNA is the rat homologue of the recently described growth arrest-specific mRNA (Gas-3), which was isolated from serum-starved 3T3 mouse fibroblasts (21,22). Both sequences show an overall homology of 92% at the nucleotide level including the 3' untranslated region.…”

mentioning

confidence: 86%

A myelin protein is encoded by the homologue of a growth arrest-specific gene.

Welcher

Suter

León

et al. 1991

Proc. Natl. Acad. Sci. U.S.A.

199

143

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Striking features of the cellular response to sciatic nerve injury are the proliferation of Schwann cells in the distal nerve stump and the downregulation of myelin-specific gene expression. Once the axons regrow, the Schwann cells differentiate again to reform the myelin sheaths. We have isolated a rat cDNA, SR13, which is strongly downregulated in the initial phase after sciatic nerve injury. This cDNA encodes a glycoprotein that shares striking amino acid similarity with a purified myelin protein and is specifically precipitated by a myelin-specific antiserum. Immunohistochemistry experiments using peptide-specific polyclonal antibodies localize the SR13 protein to the myelin sheath of the sciatic nerve. Computer-aided sequence analysis identified a pronounced homology of SR13 to a growth arrest-specific mRNA (Gas-3) that is expressed in resting but not in proliferating 3T3 mouse fibroblasts. SR13 is similarly downregulated during Schwann cell proliferation in the rat sciatic nerve. The association of the SR13 as well as the Gas-3 mRNA with nonproliferating cells in two different experimental systems suggests a common role for these molecules in maintaining the quiescent cell state.

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“…A major step in making sequence information publicly available for large-scale analysis was the formation of GenBank and its counterpart, the European Molecular Biology Laboratory data library, in 1982 (5). As more and more data is deposited, these and other databases have become increasingly useful because there is an ever greater chance of finding sequence similarity (and inferring potential homology) to a newly sequenced gene.…”

Section: Sequences and Sequence Databasesmentioning

confidence: 99%

Genomics and Synteny

McCouch

2001

Plant Physiology

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Building on early observations about natural plant variation in time and space, early geneticists, including Darwin, Mendel, and Vavilov, posed fundamental questions about the origin, structure, and evolution of genetic diversity. They postulated that an underlying reservoir of innate and heritable genetic possibilities delineated the options for the growth, development, and reproduction of organisms at both the individual and population levels. The field of plant genetics today continues to address many of the same questions while integrating developments in molecular and computational biology. Over the last 15 to 20 years, new, highly automated tools have created unprecedented opportunities for generating and analyzing large biological data sets, and the systematic processing of nucleic acid and protein sequence information from many different organisms has fundamentally changed the way that biologists approach the study of living things. GENOMICSThe term genome (derived from the words genes and chromosomes) was first used by Winkler (30) to signify the complete set of chromosomes and their genes. The term genomics was first used in 1986 to describe the enterprise that aimed to map and sequence the human genome (18). The field of genomics takes advantage of the common biological language represented by DNA and RNA and uses high throughput sequencing strategies, microchip arrays, digital technology, and computationally intensive analysis to understand the structure, function, and evolution of diverse organisms. Applications of genomic technologies in all areas of biology have lowered the barriers that once separated the plant, animal, and microbial research communities. LINKAGE MAPPINGThe use of restriction fragment length polymorphisms (RFLPs) as genetic markers made it possible to map, for the first time, an almost unlimited number of randomly distributed polymorphic loci in a single population and provided the foundation for efficient, whole-genome studies at the molecular level. The application of RFLP technology for genetic mapping was pioneered in humans by Botstein et al. (8). The distributed nature of restriction enzyme sites and the neutral nature of restriction enzyme polymorphism turned out to be equally applicable for genetic map construction in plants. This was first demonstrated by Bernatzky and Tanksley (4) and Helentjaris et al. (12), whose work established the foundation for molecular mapping in a wide variety of plant species over the next decade. QUANTITATIVE TRAIT LOCUS (QTL) ANALYSISThe advances in molecular linkage mapping unleashed a series of powerful new methodologies for studying genotype-phenotype relationships. Given the emphasis on diversity (rather than on a single species) in the plant kingdom, low-or mediumresolution molecular maps were constructed for numerous plant species over the last 15 years. One of the rationales for constructing these maps was to facilitate genetic analysis and characterization of genes underlying both simply and quantitatively inherited traits. The pla...

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The GenBank genetic sequence databank

Cited by 337 publications

References 2 publications

A mathematically designed STS primer without any mismatches for direct sequencing of cosmid DNA clones

A mathematically designed STS primer without any mismatches for direct sequencing of cosmid DNA clones

A myelin protein is encoded by the homologue of a growth arrest-specific gene.

Genomics and Synteny

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