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Title: SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

Abstract

A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 {sup 32}P- or {sup 33}P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to bemore » read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.« less

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab., IL (United States)
Sponsoring Org.:
USDOE, Washington, DC (United States)
OSTI Identifier:
10105673
Report Number(s):
ANL/BIM/CP-75997; CONF-9206273-2
ON: DE93004196
DOE Contract Number:  
W-31109-ENG-38
Resource Type:
Conference
Resource Relation:
Conference: 2. international conference on bioinformatics, supercomputing, and complex genome analysis,St. Petersburg, FL (United States),4-7 Jun 1992; Other Information: PBD: [1992]
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; GENETIC MAPPING; AUTOMATION; OLIGONUCLEOTIDES; DNA HYBRIDIZATION; IMAGE PROCESSING; DATA PROCESSING; SPECIES DIVERSITY; PHOSPHORUS 32; TRACER TECHNIQUES; 550401; 550201

Citation Formats

Drmanac, R, Drmanac, S, Labat, I, Vicentic, A, Gemmell, A, Stavropoulos, N, and Jarvis, J. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes. United States: N. p., 1992. Web.
Drmanac, R, Drmanac, S, Labat, I, Vicentic, A, Gemmell, A, Stavropoulos, N, & Jarvis, J. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes. United States.
Drmanac, R, Drmanac, S, Labat, I, Vicentic, A, Gemmell, A, Stavropoulos, N, and Jarvis, J. 1992. "SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes". United States. https://www.osti.gov/servlets/purl/10105673.
@article{osti_10105673,
title = {SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes},
author = {Drmanac, R and Drmanac, S and Labat, I and Vicentic, A and Gemmell, A and Stavropoulos, N and Jarvis, J},
abstractNote = {A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 {sup 32}P- or {sup 33}P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.},
doi = {},
url = {https://www.osti.gov/biblio/10105673}, journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Dec 01 00:00:00 EST 1992},
month = {Tue Dec 01 00:00:00 EST 1992}
}

Conference:
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