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Automatic design of gene-specific sequence tags for genome-wide functional studies

Vincent Thareau UGent, Patrice Déhais UGent, Carine Serizet UGent, Pierre Hilson UGent, Pierre Rouzé and Sébastien Aubourg UGent (2003) BIOINFORMATICS. 19(17). p.2191-2198
abstract
Motivation: The availability of complete genome sequences allows the identification of short DNA segments that are specific to each annotated gene. Such unique gene sequence tags (GSTs) replace advantageously cDNAs in microarray transcript profiling experiments. In particular, probes corresponding to individual members of multigene families can be chosen carefully to avoid cross-hybridization events. Results: The Specific Primer and Amplicon Design Software (SPADS) was constructed to delineate the more divergent regions in each gene by comparing them with a completely annotated genome sequence and to select optimal primer pairs for the polymerase chain reaction amplification of one divergent region per gene. SPADS is a unique integrated tool to design specific GSTs from any public or private genome sequences and allows the user to fine-tune GIST size and specificity. SPADS has been used to obtain probes for whole genome and family-wide transcript profiling, as well as inserts for gene-specific knock-out experiments.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
DATABASE, SELECTION, ARRAYS, GENERATION, DUPLICATION, CROSS-HYBRIDIZATION, MICROARRAY ANALYSIS
journal title
BIOINFORMATICS
Bioinformatics
volume
19
issue
17
pages
2191 - 2198
Web of Science type
Article
Web of Science id
000186919200004
JCR category
COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS
JCR impact factor
6.701 (2003)
JCR rank
1/81 (2003)
JCR quartile
1 (2003)
ISSN
1367-4803
DOI
10.1093/bioinformatics/btg286
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
212302
handle
http://hdl.handle.net/1854/LU-212302
date created
2004-04-22 14:59:00
date last changed
2016-12-19 15:38:14
@article{212302,
  abstract     = {Motivation: The availability of complete genome sequences allows the identification of short DNA segments that are specific to each annotated gene. Such unique gene sequence tags (GSTs) replace advantageously cDNAs in microarray transcript profiling experiments. In particular, probes corresponding to individual members of multigene families can be chosen carefully to avoid cross-hybridization events.
Results: The Specific Primer and Amplicon Design Software (SPADS) was constructed to delineate the more divergent regions in each gene by comparing them with a completely annotated genome sequence and to select optimal primer pairs for the polymerase chain reaction amplification of one divergent region per gene. SPADS is a unique integrated tool to design specific GSTs from any public or private genome sequences and allows the user to fine-tune GIST size and specificity. SPADS has been used to obtain probes for whole genome and family-wide transcript profiling, as well as inserts for gene-specific knock-out experiments.},
  author       = {Thareau, Vincent and D{\'e}hais, Patrice and Serizet, Carine and Hilson, Pierre and Rouz{\'e}, Pierre and Aubourg, S{\'e}bastien},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keyword      = {DATABASE,SELECTION,ARRAYS,GENERATION,DUPLICATION,CROSS-HYBRIDIZATION,MICROARRAY ANALYSIS},
  language     = {eng},
  number       = {17},
  pages        = {2191--2198},
  title        = {Automatic design of gene-specific sequence tags for genome-wide functional studies},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btg286},
  volume       = {19},
  year         = {2003},
}

Chicago
Thareau, Vincent, Patrice Déhais, Carine Serizet, Pierre Hilson, Pierre Rouzé, and Sébastien Aubourg. 2003. “Automatic Design of Gene-specific Sequence Tags for Genome-wide Functional Studies.” Bioinformatics 19 (17): 2191–2198.
APA
Thareau, V., Déhais, P., Serizet, C., Hilson, P., Rouzé, P., & Aubourg, S. (2003). Automatic design of gene-specific sequence tags for genome-wide functional studies. BIOINFORMATICS, 19(17), 2191–2198.
Vancouver
1.
Thareau V, Déhais P, Serizet C, Hilson P, Rouzé P, Aubourg S. Automatic design of gene-specific sequence tags for genome-wide functional studies. BIOINFORMATICS. 2003;19(17):2191–8.
MLA
Thareau, Vincent, Patrice Déhais, Carine Serizet, et al. “Automatic Design of Gene-specific Sequence Tags for Genome-wide Functional Studies.” BIOINFORMATICS 19.17 (2003): 2191–2198. Print.