A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
FLAGdb++: a database for the functional analysis of the Arabidopsis genome
2004
Nucleic Acids Research
Preserved Fulltext
FLAGdb ++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis. ...
FLAGdb ++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and speci®cities having an impact upon the con-®dence we will put in the ...
ACKNOWLEDGEMENTS The authors are grateful to collaborators for producing the biological data or computer predictions integrated into FLAGdb ++ ...
doi:10.1093/nar/gkh134
pmid:14681431
pmcid:PMC308868
fatcat:63ovrr3txrbbzmrufoezjp554e
Exploration of plant genomes in the FLAGdb++ environment
2011
Plant Methods
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Conclusion: Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb ++ presents a powerful complementary tool for exploring plant ...
In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. ...
The development of FLAGdb ++ has been supported in part by ANR and Génoplante projects. ...
doi:10.1186/1746-4811-7-8
pmid:21447150
pmcid:PMC3073958
fatcat:ou5iw7mktzf4popielzchrcvqa
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions
2007
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
A graphic display of the genome region around the gene or the FST assists users to select insertion lines of their interests. ...
Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. ...
at MPI for Plant Breeding Research and the Chair of Genome Research at Bielefeld University for sequencing. ...
doi:10.1093/nar/gkl753
pmid:17062622
pmcid:PMC1781121
fatcat:awjipf4tujd5lossgxdh34x5sq
Site Preferences of Insertional Mutagenesis Agents in Arabidopsis
2005
Plant Physiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
We have performed a comparative analysis of the insertion sites of engineered Arabidopsis (Arabidopsis thaliana) insertional mutagenesis vectors that are based on the maize (Zea mays) transposable elements ...
The transposon-based agents show a bias toward insertions near the translation start codons of genes, while the T-DNAs show a predilection for the putative transcriptional regulatory regions of genes. ...
Research, Germany, the FLAGdb/FST, France, and the Institute of Molecular Agrobiology, Singapore for allowing us to use their insertional mutagenesis data. ...
doi:10.1104/pp.104.053215
pmid:15618417
pmcid:PMC548848
fatcat:t25hl3wwmbgefktjvsnf2y6754
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
2007
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We acknowledge Franck Samson for FLAGdb ++ developments, Carine Serizet for the Eugene v1.59 annotation of the Arabidopsis genome, and Joan Sobota for correcting the manuscript. ...
Acknowledgements We are grateful to all the CATMA partners and collaborators for the making of the micro-arrays and all the transcriptome projects used in the study. ...
FLAGdb ++ also contains TAIR gene annota-tions, available transcript sequences and the latest version of the Eugene predictions (v1.59) for the Arabidopsis genome. ...
doi:10.1186/1471-2164-8-401
pmid:17980019
pmcid:PMC2174955
fatcat:x4hh3z4y7jhi3akdalhy2bcgbe
Page 935 of Cellular and Molecular Life Sciences Vol. 60, Issue 5
[page]
2003
Cellular and Molecular Life Sciences
Preserved Fulltext
The Internet Archive has digitized a microfilm copy of this work. It may be possible to borrow a copy for reading.
Bot. 52: 1593-1601
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. ...
., Pelletier G. et al. (2002) FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants. ...
GenoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
2003
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis ...
programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). ...
We are very grateful to our Génoplante colleagues for the submission of their data and/or tools to GPI, their participation in many bioinformatics meetings and task forces, and for their help in defining ...
doi:10.1093/nar/gkg060
pmid:12519976
pmcid:PMC165507
fatcat:2rggwjp6xbh3re6whcjibiblea
Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions
2006
Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Large collections of sequence-indexed T-DNA insertion mutants are invaluable resources for plant functional genomics. ...
Flanking sequence tag (FST) data from these collections indicated that T-DNA insertions are not randomly distributed in the Arabidopsis thaliana genome and that there are still a fairly high number of ...
This work was supported by the BMBF in the context of the German plant genomics program GABI (Förderkennzeichen 0312273). ...
doi:10.1016/j.ygeno.2005.12.010
pmid:16488113
fatcat:hnig3bxqsrap7ec3izncxp6via
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform
2007
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
ACKNOWLEDGEMENTS The authors would like to thank Franck Samson for his help during the optimization of the code and Philippe Grevet for assistance and management of the ftp and web servers. ...
Funding to pay the Open Access publication charges for this article was provided by INRA. The URGV CATMA resource has been funded by Ge´noplante. ...
Database (SMD) (4, 5) and (iii) specific databases dedicated to a species like The Arabidopsis Information Resource, or the expression browser (eFP) from the Bio-Array Resource for Arabidopsis Functional ...
doi:10.1093/nar/gkm757
pmid:17940091
pmcid:PMC2238931
fatcat:2lh3ut2s2baido5ifdszhkatje
ATIDB: Arabidopsis thaliana insertion database
2003
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Tools integrated with the database include a graphical genome browser, a protein search function, a graphical representation of the insertion distribution and a Blast search function. ...
Users can search the database to identify insertions in a particular gene or perform genome-wide analysis to study the distribution and preference of insertions. ...
at Cold Spring Harbor Laboratory, NY, for part of the insertion data. ...
doi:10.1093/nar/gkg222
pmid:12582244
pmcid:PMC150240
fatcat:gzv6zm6vybbylaioj5e77kjw7u
Phenome Analysis in Plant Species Using Loss-of-Function and Gain-of-Function Mutants
2009
Plant and Cell Physiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Acknowledgments The authors are grateful to Drs. ...
Hirohiko Hirochika, Hiroaki Ichikawa, Takanari Ichikawa, Hiroshi Takatsuji, Masaki Mori, Kenji Oda, Hidetaka Kaya, Tetsuya Sakurai, Masanori Tamaoki and Takashi Hirayama for their valuable suggestions ...
As a result, a large number of T-DNA or transposon-insertional lines have already been prepared for functional genomics in Arabidopsis. ...
doi:10.1093/pcp/pcp078
pmid:19502383
pmcid:PMC2709550
fatcat:pcorqrag7jgmppgdftxqx3wece
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
2004
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database ...
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. ...
ACKNOWLEDGEMENTS The authors are grateful to Vincent Thareau for his help in the comparison between the GeneFarm and TIGR annotations. The GeneFarm database has been filed at the 'Agence pour la ...
doi:10.1093/nar/gki115
pmid:15608279
pmcid:PMC540069
fatcat:5i6iv33sffhmdgzsbedb2ggtpa
Transgenic Plants as Gene-Discovery Tools
[chapter]
2012
Transgenic Plants - Advances and Limitations
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Loss-of-function mutations The most conventional tool for the functional analysis of all genes in a certain organism is to generate indexed loss-of-function mutagenesis on a whole genome scale. ...
functions at a genome wide level. ...
Transgenic Plants -Advances and Limitations Development of efficient transformation protocols is becoming a complementary strategy to conventional breeding techniques for the improvement of crops. ...
doi:10.5772/33895
fatcat:q257532djbeixbf255usafill4
An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches
2009
BMC Plant Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Functional genomics tools provide researchers with the ability to apply high-throughput techniques to determine the function and interaction of a diverse range of genes. ...
Arabidopsis genome sequence http://aafc-aac.usask.ca/FST. ...
Acknowledgements The work described was supported by funding from AAFC Canadian Crop Genomics Initiative grants to IAPP and MYG, in addition YYW was partially supported by an NSERC discovery grant to SR ...
doi:10.1186/1471-2229-9-101
pmid:19646253
pmcid:PMC3091532
fatcat:3mzd2mkrt5envhxvugse4prfxe
OryGenesDB: a database for rice reverse genetics
2006
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. ...
As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors. ...
We acknowledge the support of the EU 5th framework project QLG2-CT-2001-01453 CerealGene Tags and of the Generation Challenge Program. ...
doi:10.1093/nar/gkj012
pmid:16381969
pmcid:PMC1347375
fatcat:mxpilrarl5am5i4gf42whsvhky
« Previous
Showing results 1 — 15 out of 89 results