Document Detail


The construction of an EST database for Bombyx mori and its application.
MedLine Citation:
PMID:  14614147     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
To build a foundation for the complete genome analysis of Bombyx mori, we have constructed an EST database. Because gene expression patterns deeply depend on tissues as well as developmental stages, we analyzed many cDNA libraries prepared from various tissues and different developmental stages to cover the entire set of Bombyx genes. So far, the Bombyx EST database contains 35,000 ESTs from 36 cDNA libraries, which are grouped into approximately 11,000 nonredundant ESTs with the average length of 1.25 kb. The comparison with FlyBase suggests that the present EST database, SilkBase, covers >55% of all genes of Bombyx. The fraction of library-specific ESTs in each cDNA library indicates that we have not yet reached saturation, showing the validity of our strategy for constructing an EST database to cover all genes. To tackle the coming saturation problem, we have checked two methods, subtraction and normalization, to increase coverage and decrease the number of housekeeping genes, resulting in a 5-11% increase of library-specific ESTs. The identification of a number of genes and comprehensive cloning of gene families have already emerged from the SilkBase search. Direct links of SilkBase with FlyBase and WormBase provide ready identification of candidate Lepidoptera-specific genes.
Authors:
Kazuei Mita; Mitsuoki Morimyo; Kazuhiro Okano; Yoshiko Koike; Junko Nohata; Hideki Kawasaki; Keiko Kadono-Okuda; Kimiko Yamamoto; Masataka G Suzuki; Toru Shimada; Marian R Goldsmith; Susumu Maeda
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2003-11-12
Journal Detail:
Title:  Proceedings of the National Academy of Sciences of the United States of America     Volume:  100     ISSN:  0027-8424     ISO Abbreviation:  Proc. Natl. Acad. Sci. U.S.A.     Publication Date:  2003 Nov 
Date Detail:
Created Date:  2003-12-03     Completed Date:  2004-02-02     Revised Date:  2013-06-09    
Medline Journal Info:
Nlm Unique ID:  7505876     Medline TA:  Proc Natl Acad Sci U S A     Country:  United States    
Other Details:
Languages:  eng     Pagination:  14121-6     Citation Subset:  IM    
Affiliation:
Laboratory of Insect Genome, National Institute of Agrobiological Sciences, Owashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Animals
Bombyx / genetics*
Chromosomes, Artificial, Bacterial / genetics
DNA, Complementary / genetics
Databases, Genetic*
Expressed Sequence Tags*
Gene Library
Insect Proteins / genetics
Molecular Sequence Data
Sequence Homology, Amino Acid
Chemical
Reg. No./Substance:
0/DNA, Complementary; 0/Insect Proteins
Comments/Corrections

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