Advanced search
1 file | 368.73 KB

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 (UGent) and Sébastien Aubourg (UGent)
(2003) BIOINFORMATICS. 19(17). p.2191-2198
Author
Organization
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.
Keywords
DATABASE, SELECTION, ARRAYS, GENERATION, DUPLICATION, CROSS-HYBRIDIZATION, MICROARRAY ANALYSIS

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 368.73 KB

Citation

Please use this url to cite or link to this publication:

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.
@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},
}

Altmetric
View in Altmetric
Web of Science
Times cited: