GeneFisher--software support for the detection of postulated genes

Giegerich R, Meyer F, Schleiermacher C (1996)
Proc Int Conf Intell Syst Mol Biol 4: 68-77.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Giegerich, RobertUniBi; Meyer, Folker; Schleiermacher, Chris
Einrichtung
Technische Fakultät > AG Praktische Informatik
Abstract / Bemerkung
When a family of genes from closely related organisms is known, there is a certain change to extract the corresponding gene from the genome of another related organism. This can be done by polymerase chain reaction, provided that a pair of suitable primers can be designed. In contrast to primer design for a single, known target sequence, systematic primer design for an unknown target given a group of homologues can by no means be done manually. GeneFisher is a software tool which automates this task, and takes special care to make the impact of the manifold design parameters transparent to the user.
Erscheinungsjahr
1996
Zeitschriftentitel
Proc Int Conf Intell Syst Mol Biol
Band
4
Seite(n)
68-77
ISSN
1553-0833
Page URI
https://pub.uni-bielefeld.de/record/1947921

Zitieren

Giegerich R, Meyer F, Schleiermacher C. GeneFisher--software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol. 1996;4:68-77.
Giegerich, R., Meyer, F., & Schleiermacher, C. (1996). GeneFisher--software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol, 4, 68-77.
Giegerich, Robert, Meyer, Folker, and Schleiermacher, Chris. 1996. “GeneFisher--software support for the detection of postulated genes”. Proc Int Conf Intell Syst Mol Biol 4: 68-77.
Giegerich, R., Meyer, F., and Schleiermacher, C. (1996). GeneFisher--software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol 4, 68-77.
Giegerich, R., Meyer, F., & Schleiermacher, C., 1996. GeneFisher--software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol, 4, p 68-77.
R. Giegerich, F. Meyer, and C. Schleiermacher, “GeneFisher--software support for the detection of postulated genes”, Proc Int Conf Intell Syst Mol Biol, vol. 4, 1996, pp. 68-77.
Giegerich, R., Meyer, F., Schleiermacher, C.: GeneFisher--software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol. 4, 68-77 (1996).
Giegerich, Robert, Meyer, Folker, and Schleiermacher, Chris. “GeneFisher--software support for the detection of postulated genes”. Proc Int Conf Intell Syst Mol Biol 4 (1996): 68-77.

61 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Genome organization and molecular characterization of the three Formica exsecta viruses-FeV1, FeV2 and FeV4.
Dhaygude K, Johansson H, Kulmuni J, Sundström L., PeerJ 6(), 2019
PMID: 30809424
Association of genetic polymorphisms in SOD2, SOD3, GPX3, and GSTT1 with hypertriglyceridemia and low HDL-C level in subjects with high risk of coronary artery disease.
Decharatchakul N, Settasatian C, Settasatian N, Komanasin N, Kukongviriyapan U, Intharaphet P, Senthong V., PeerJ 7(), 2019
PMID: 31396447
Microsatellites within the feline androgen receptor are suitable for X chromosome-linked clonality testing in archival material.
Farwick NM, Klopfleisch R, Gruber AD, Weiss AT., J Feline Med Surg 19(4), 2017
PMID: 26919893
Quantification of Chloroflexi Eikelboom morphotype 1851 for prediction and control of bulking events in municipal activated sludge plants in Japan.
Nittami T, Speirs LBM, Yamada T, Suzuki I, Fukuda J, Kurisu F, Seviour RJ., Appl Microbiol Biotechnol 101(9), 2017
PMID: 28093622
Endogenous Natural Complement Inhibitor Regulates Cardiac Development.
Mortensen SA, Skov LL, Kjaer-Sorensen K, Hansen AG, Hansen S, Dagnæs-Hansen F, Jensenius JC, Oxvig C, Thiel S, Degn SE., J Immunol 198(8), 2017
PMID: 28258200
Using Real-Time PCR as a tool for monitoring the authenticity of commercial coffees.
Ferreira T, Farah A, Oliveira TC, Lima IS, Vitório F, Oliveira EM., Food Chem 199(), 2016
PMID: 26775992
Effect of osmopriming on germination and initial growth of Physalis angulata L. under salt stress and on expression of associated genes.
Souza MO, Pelacani CR, Willems LA, Castro RD, Hilhorst HW, Ligterink W., An Acad Bras Cienc 88 Suppl 1(), 2016
PMID: 27142542
Surfactant dysfunction during overexpression of TGF-β1 precedes profibrotic lung remodeling in vivo.
Lopez-Rodriguez E, Boden C, Echaide M, Perez-Gil J, Kolb M, Gauldie J, Maus UA, Ochs M, Knudsen L., Am J Physiol Lung Cell Mol Physiol 310(11), 2016
PMID: 27106287
Designing Polymerase Chain Reaction Primers Using Primer3Plus.
Hung JH, Weng Z., Cold Spring Harb Protoc 2016(9), 2016
PMID: 27574202
PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.
Yoon H, Leitner T., Bioinformatics 31(9), 2015
PMID: 25524896
MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR.
Kim H, Kang N, Chon KW, Kim S, Lee N, Koo J, Kim MS., Nucleic Acids Res 43(20), 2015
PMID: 26109350
Two genomic regions together cause dark abdominal pigmentation in Drosophila tenebrosa.
Bray MJ, Werner T, Dyer KA., Heredity (Edinb) 112(4), 2014
PMID: 24326291
Association of IRGM gene mutations with inflammatory bowel disease in the Indian population.
Baskaran K, Pugazhendhi S, Ramakrishna BS., PLoS One 9(9), 2014
PMID: 25191865
Selection of proper reference genes for the cyanobacterium Synechococcus PCC 7002 using real-time quantitative PCR.
Szekeres E, Sicora C, Dragoş N, Drugă B., FEMS Microbiol Lett 359(1), 2014
PMID: 25115691
Perinatal manipulation of α-linolenic acid intake induces epigenetic changes in maternal and offspring livers.
Niculescu MD, Lupu DS, Craciunescu CN., FASEB J 27(1), 2013
PMID: 22997227
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.
Brodin J, Krishnamoorthy M, Athreya G, Fischer W, Hraber P, Gleasner C, Green L, Korber B, Leitner T., BMC Bioinformatics 14(), 2013
PMID: 23965160
Expanding the cyanuric acid hydrolase protein family to the fungal kingdom.
Dodge AG, Preiner CS, Wackett LP., J Bacteriol 195(23), 2013
PMID: 24039269
Chronic nicotine induces hypoxia inducible factor-2α in perinatal rat adrenal chromaffin cells: role in transcriptional upregulation of KATP channel subunit Kir6.2.
Salman S, Brown ST, Nurse CA., Am J Physiol Cell Physiol 302(10), 2012
PMID: 22403787
In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae.
Gardès J, Croce O, Christen R., Microbes Environ 27(3), 2012
PMID: 22673304
Lactobacillaceae and cell adhesion: genomic and functional screening.
Turpin W, Humblot C, Noordine ML, Thomas M, Guyot JP., PLoS One 7(5), 2012
PMID: 22675431
Opsin evolution in damselfish: convergence, reversal, and parallel evolution across tuning sites.
Hofmann CM, Marshall NJ, Abdilleh K, Patel Z, Siebeck UE, Carleton KL., J Mol Evol 75(3-4), 2012
PMID: 23080353
High prevalence of Sarcocystis calchasi sporocysts in European Accipiter hawks.
Olias P, Olias L, Krücken J, Lierz M, Gruber AD., Vet Parasitol 175(3-4), 2011
PMID: 21074324
Intron-specific neuropeptide probes.
Gainer H, Ponzio TA, Yue C, Kawasaki M., Methods Mol Biol 789(), 2011
PMID: 21922402
Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.
Tubio JM, Tojo M, Bassaganyas L, Escaramis G, Sharakhov IV, Sharakhova MV, Tornador C, Unger MF, Naveira H, Costas J, Besansky NJ., PLoS One 6(1), 2011
PMID: 21283637
Real-time PCR (qPCR) primer design using free online software.
Thornton B, Basu C., Biochem Mol Biol Educ 39(2), 2011
PMID: 21445907
The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae).
Vierna J, Jensen KT, Martínez-Lage A, González-Tizón AM., Heredity (Edinb) 107(2), 2011
PMID: 21364693
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Kalendar R, Lee D, Schulman AH., Genomics 98(2), 2011
PMID: 21569836
Exploiting expressed sequence tag databases for the development and characterization of gene-derived simple sequence repeat markers in the opium poppy (Papaver somniferum L.) for forensic applications.
Lee EJ, Jin GN, Lee KL, Han MS, Lee YH, Yang MS., J Forensic Sci 56(5), 2011
PMID: 21595695
Sarcocystis calchasi-associated neurologic disease in a domestic pigeon in North America.
Wünschmann A, Armien AG, Reed L, Gruber AD, Olias P., Transbound Emerg Dis 58(6), 2011
PMID: 21848932
Genetic screening of functional properties of lactic acid bacteria in a fermented pearl millet slurry and in the metagenome of fermented starchy foods.
Turpin W, Humblot C, Guyot JP., Appl Environ Microbiol 77(24), 2011
PMID: 22003019
Regulation of activin A synthesis in microglial cells: pathophysiological implications for bacterial meningitis.
Wilms H, Schwark T, Brandenburg LO, Sievers J, Dengler R, Deuschl G, Lucius R., J Neurosci Res 88(1), 2010
PMID: 19681171
PRAS40 regulates protein synthesis and cell cycle in C2C12 myoblasts.
Kazi AA, Lang CH., Mol Med 16(9-10), 2010
PMID: 20464060
Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5'UTR.
Jooste AE, Maree HJ, Bellstedt DU, Goszczynski DE, Pietersen G, Burger JT., Arch Virol 155(12), 2010
PMID: 20830600
Molecular cloning of cyanobacterial pteridine glycosyltransferases that catalyze the transfer of either glucose or xylose to tetrahydrobiopterin.
Lee YG, Kim AH, Park MB, Kim HL, Lee KH, Park YS., Appl Environ Microbiol 76(22), 2010
PMID: 20851980
Alcohol-induced decrease in muscle protein synthesis associated with increased binding of mTOR and raptor: Comparable effects in young and mature rats.
Lang CH, Pruznak AM, Nystrom GJ, Vary TC., Nutr Metab (Lond) 6(), 2009
PMID: 19154606
Rapid effects of 17beta-estradiol on TRPV5 epithelial Ca2+ channels in rat renal cells.
Irnaten M, Blanchard-Gutton N, Praetorius J, Harvey BJ., Steroids 74(8), 2009
PMID: 19463684
Hypoxia inducible factor (HIF)-2 alpha is required for the development of the catecholaminergic phenotype of sympathoadrenal cells.
Brown ST, Kelly KF, Daniel JM, Nurse CA., J Neurochem 110(2), 2009
PMID: 19457096
Neurotransmitter regulation of c-fos and vasopressin gene expression in the rat supraoptic nucleus.
Kawasaki M, Ponzio TA, Yue C, Fields RL, Gainer H., Exp Neurol 219(1), 2009
PMID: 19463813
Chronic nicotine blunts hypoxic sensitivity in perinatal rat adrenal chromaffin cells via upregulation of KATP channels: role of alpha7 nicotinic acetylcholine receptor and hypoxia-inducible factor-2alpha.
Buttigieg J, Brown S, Holloway AC, Nurse CA., J Neurosci 29(22), 2009
PMID: 19494136
Long-term evolution of 5S ribosomal DNA seems to be driven by birth-and-death processes and selection in Ensis razor shells (Mollusca: Bivalvia).
Vierna J, González-Tizón AM, Martínez-Lage A., Biochem Genet 47(9-10), 2009
PMID: 19633948
Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions.
Dal Cin V, Kevany B, Fei Z, Klee HJ., Theor Appl Genet 119(7), 2009
PMID: 19680624
Regulation of REDD1 by insulin-like growth factor-I in skeletal muscle and myotubes.
Frost RA, Huber D, Pruznak A, Lang CH., J Cell Biochem 108(5), 2009
PMID: 19795384
Chronic alcohol accentuates simian acquired immunodeficiency syndrome-associated wasting.
Molina PE, Lang CH, McNurlan M, Bagby GJ, Nelson S., Alcohol Clin Exp Res 32(1), 2008
PMID: 18028526
Sepsis and AMPK Activation by AICAR Differentially Regulate FoxO-1, -3 and -4 mRNA in Striated Muscle.
Nystrom GJ, Lang CH., Int J Clin Exp Med 1(1), 2008
PMID: 19079687
Detection of bovine babesiosis in Mozambique by a novel seminested hot-start PCR method.
Martins TM, Pedro OC, Caldeira RA, do Rosário VE, Neves L, Domingos A., Vet Parasitol 153(3-4), 2008
PMID: 18329810
Acute alcohol intoxication increases REDD1 in skeletal muscle.
Lang CH, Frost RA, Vary TC., Alcohol Clin Exp Res 32(5), 2008
PMID: 18336631
Rapid effects of 17beta-estradiol on epithelial TRPV6 Ca2+ channel in human T84 colonic cells.
Irnaten M, Blanchard-Gutton N, Harvey BJ., Cell Calcium 44(5), 2008
PMID: 18395250
Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium.
Pratt CH, Vadigepalli R, Chakravarthula P, Gonye GE, Philp NJ, Grunwald GB., Mol Vis 14(), 2008
PMID: 18682805
PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences.
Yao J, Lin H, Van Deynze A, Doddapaneni H, Francis M, Lemos EG, Civerolo EL., BMC Microbiol 8(), 2008
PMID: 18937861
Characterization of Treponema denticola pyrF encoding orotidine-5'-monophosphate decarboxylase.
Capone RF, Ning Y, Pakulis N, Alhazzazi T, Fenno JC., FEMS Microbiol Lett 268(2), 2007
PMID: 17187656
An intron-based real-time PCR method for measuring vasopressin gene transcription.
Ponzio TA, Yue C, Gainer H., J Neurosci Methods 164(1), 2007
PMID: 17540451
Nicotine modulation of cytokine induction by LPS-stimulated human monocytes and coronary artery endothelial cells.
Patton GW, Powell DA, Hakki A, Friedman H, Pross S., Int Immunopharmacol 6(1), 2006
PMID: 16332510
Recent developments in primer design for DNA polymorphism and mRNA profiling in higher plants.
Yang X, Scheffler BE, Weston LA., Plant Methods 2(1), 2006
PMID: 16509990
Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.
Jabado OJ, Palacios G, Kapoor V, Hui J, Renwick N, Zhai J, Briese T, Lipkin WI., Nucleic Acids Res 34(22), 2006
PMID: 17135211
Gene expression profiling of choline-deprived neural precursor cells isolated from mouse brain.
Niculescu MD, Craciunescu CN, Zeisel SH., Brain Res Mol Brain Res 134(2), 2005
PMID: 15836926
Identification of genes potentially involved in disease transformation of CML.
Janssen JJ, Klaver SM, Waisfisz Q, Pasterkamp G, de Kleijn DP, Schuurhuis GJ, Ossenkoppele GJ., Leukemia 19(6), 2005
PMID: 15815727
A CDP-choline pathway for phosphatidylcholine biosynthesis in Treponema denticola.
Kent C, Gee P, Lee SY, Bian X, Fenno JC., Mol Microbiol 51(2), 2004
PMID: 14756787
Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao.
Borrone JW, Kuhn DN, Schnell RJ., Theor Appl Genet 109(3), 2004
PMID: 15148571
Recent radiation of endemic Caribbean Drosophila of the dunni subgroup inferred from multilocus DNA sequence variation.
Wilder JA, Hollocher H., Evolution 57(11), 2003
PMID: 14686532
Involvement of benzodiazepine receptors in neuroinflammatory and neurodegenerative diseases: evidence from activated microglial cells in vitro.
Wilms H, Claasen J, Röhl C, Sievers J, Deuschl G, Lucius R., Neurobiol Dis 14(3), 2003
PMID: 14678758
Cleavage of Treponema denticola PrcA polypeptide to yield protease complex-associated proteins Prca1 and Prca2 is dependent on PrtP.
Lee SY, Bian XL, Wong GW, Hannam PM, McBride BC, Fenno JC., J Bacteriol 184(14), 2002
PMID: 12081957
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Quellen

PMID: 8877506
PubMed | Europe PMC

Suchen in

Google Scholar