FindGDPs：用于标记微生物转录组以进行DNA微阵列分析的引物鉴定
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis.
作者信息
Blick Robert J, Revel Andrew T, Hansen Eric J
机构信息
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA.
出版信息
Bioinformatics. 2003 Sep 1;19(13):1718-9. doi: 10.1093/bioinformatics/btg218.
Abstract
FindGDPs is a program that uses a greedy algorithm to quickly identify a set of genome-directed primers that specifically anneal to all of the open reading frames ina genome and that do not exhibit full-length complementarity to the members of another user-supplied set of nucleotide sequences.
摘要
FindGDPs是一个程序，它使用贪心算法来快速识别一组基因组导向引物，这些引物能特异性地与基因组中的所有开放阅读框退火，并且与另一组用户提供的核苷酸序列成员不存在全长互补性。
相似文献
1
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis.
Bioinformatics. 2003 Sep 1;19(13):1718-9. doi: 10.1093/bioinformatics/btg218.
2
Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis.
Nat Biotechnol. 2000 Jun;18(6):679-82. doi: 10.1038/76543.
3
G-PRIMER: greedy algorithm for selecting minimal primer set.
Bioinformatics. 2004 Oct 12;20(15):2473-5. doi: 10.1093/bioinformatics/bth259. Epub 2004 Apr 8.
4
Oligo Design: a computer program for development of probes for oligonucleotide microarrays.
Biotechniques. 2003 Dec;35(6):1216-21. doi: 10.2144/03356bc02.
5
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.
Bioinformatics. 2002 Nov;18(11):1432-7. doi: 10.1093/bioinformatics/18.11.1432.
6
PROBEmer: A web-based software tool for selecting optimal DNA oligos.
Nucleic Acids Res. 2003 Jul 1;31(13):3746-50. doi: 10.1093/nar/gkg569.
7
Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays.
Bioinformatics. 2007 Jan 1;23(1):5-13. doi: 10.1093/bioinformatics/btl549. Epub 2006 Oct 26.
8
ArrayNorm: comprehensive normalization and analysis of microarray data.
Bioinformatics. 2004 Aug 12;20(12):1971-3. doi: 10.1093/bioinformatics/bth174. Epub 2004 Apr 8.
9
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.
BMC Genomics. 2009 Dec 3;10 Suppl 3(Suppl 3):S4. doi: 10.1186/1471-2164-10-S3-S4.
10
Genome-scale probe and primer design with PRIMEGENS.
Methods Mol Biol. 2007;402:159-76. doi: 10.1007/978-1-59745-528-2_8.
引用本文的文献
1
Regulation of expression of the Haemophilus ducreyi LspB and LspA2 proteins by CpxR.
Infect Immun. 2009 Aug;77(8):3402-11. doi: 10.1128/IAI.00292-09. Epub 2009 May 18.
2
An evaluation of custom microarray applications: the oligonucleotide design challenge.
Nucleic Acids Res. 2009 Apr;37(6):1726-39. doi: 10.1093/nar/gkp053. Epub 2009 Feb 10.
3
Metabolic analysis of Moraxella catarrhalis and the effect of selected in vitro growth conditions on global gene expression.
Infect Immun. 2007 Oct;75(10):4959-71. doi: 10.1128/IAI.00073-07. Epub 2007 Jul 9.
4
Identification of Francisella tularensis genes affected by iron limitation.
Infect Immun. 2006 Jul;74(7):4224-36. doi: 10.1128/IAI.01975-05.
5
Genome-wide selection of unique and valid oligonucleotides.
Nucleic Acids Res. 2005 Jul 26;33(13):e115. doi: 10.1093/nar/gni110.
本文引用的文献
1
Priming reverse transcription with oligo(dT) does not yield representative samples of Mycobacterium tuberculosis cDNA.
Microbiology (Reading). 2002 Aug;148(Pt 8):2567-2572. doi: 10.1099/00221287-148-8-2567.
2
Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis.
Nat Biotechnol. 2000 Jun;18(6):679-82. doi: 10.1038/76543.
3
Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization.
Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12833-8. doi: 10.1073/pnas.96.22.12833.
4
Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
Science. 1995 Oct 20;270(5235):467-70. doi: 10.1126/science.270.5235.467.
Zotero 插件