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


BACKGROUND
The GENOPLANTE SPADS source code and web interface are available upon request. The online version is accessible via http://genoplante-info.infobiogen.fr/spads and via http://oberon.fvms.ugent.be:8080/SPADS/
Thareau
Vincent
V
Laboratoire Associé de l'Institut National de Recherche Agronomique, France.
Déhais
Patrice
P
Serizet
Carine
C
Hilson
Pierre
P
Rouzé
Pierre
P
Aubourg
Sébastien
S
D000465:Algorithms; D015342:DNA Probes / Q000737:chemistry* / Q000235:genetics; D020224:Expressed Sequence Tags / Q000737:chemistry*; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D016247:Information Storage and Retrieval; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes