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PMID: 9110174 Published · ppublish English Letter Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Large-scale concatenation cDNA sequencing.

Genome research ·Vol. 7 ·No. 4 ·1997-04-00 ·Pages 353-8

Yu W, Andersson B, Worley KC, Muzny DM, Ding Y, Liu W, Ricafrente JY, Wentland MA, Lennon G, Gibbs RA

Abstract

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7-2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (> 20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (> or = 98% identity), and 16 clones generated nonexact matches (57%-97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching.

MeSH Terms
DNA Transposable Elements DNA, Complementary/chemistry,genetics Databases, Factual Gene Library Humans Molecular Sequence Data Proteins/chemistry,genetics Sequence Alignment/methods Sequence Analysis, DNA/methods Sequence Homology, Amino Acid Sequence Homology, Nucleic Acid Software
Chemicals
DNA Transposable Elements DNA, Complementary Proteins
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Yu W
Andersson B
Worley K C
Muzny D M
Ding Y
Liu W
Ricafrente J Y
Wentland M A
Lennon G
Gibbs R A
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.7.4.353
Published
1997-04-00
Pages
353-8
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC139146
Subset
IM
Grants
NHGRI NIH HHS · P30 HG00210-05 · United States
NHGRI NIH HHS · R01 HG00823 · United States
NHGRI NIH HHS · 1F32 HG00169-01 · United States
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GENBANK
AF007128, AF007129, AF007130, AF007131, AF007132, AF007133, AF007134, AF007135, AF007136, AF007137, AF007138, AF007139, AF007140, AF007141, AF007142, AF007143, AF007144, AF007145, AF007146, AF007147, AF007148, AF007149, AF007150, AF007151, AF007152, AF007153, AF007154
External Links
PubMed source DOI: 10.1101/gr.7.4.353 PMC Full Text View journal details
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