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Protocols

MAtDB specifications

Information


Unique identifier OMICS_15020
Name MAtDB
Alternative name MIPS Arabidopsis thaliana Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

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Publication for MIPS Arabidopsis thaliana Database

MAtDB citations

 (9)
call_split

Using the Yeast Three Hybrid System to Identify Proteins that Interact with a Phloem Mobile mRNA

2012
Front Plant Sci
PMCID: 3427875
PMID: 22969782
DOI: 10.3389/fpls.2012.00189
call_split See protocol

[…] atabase. Translated protein sequences were obtained from Translate and ORF Finder and analyzed using BLAST on the TAIR database. Functional categorization of selected proteins was performed using the MIPS Arabidopsis thaliana database. The domains of the B5RBPs (Figure ) were analyzed using SMART and NCBI’s Conserved Domain Search. For Figure A, amino acid sequences of Arabidopsis and potato LSH p […]

library_books

Genome wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis

2008
BMC Genomics
PMCID: 2612031
PMID: 19021904
DOI: 10.1186/1471-2164-9-550

[…] To collect all members of the PP2C gene family in Arabidopsis, an initial keyword search was performed using "protein phosphatase 2C" to screen six databases, i.e. NCBI [], DATF [], MAtDB [], TAIR [], TIGR [] and PlantsP []. The resulting protein hits were pooled together and redundant sequences were removed using a custom Perl program. Remaining proteins sequences were then used […]

library_books

An extensive (co )expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana

2008
BMC Plant Biol
PMCID: 2383897
PMID: 18433503
DOI: 10.1186/1471-2229-8-47

[…] File and at the 'CYPedia' homepage. A description of their biochemical function is also given (if known) and links to relevant publications as well as to information in external databases, such as 'MAtDB, 'TAIR', or 'SIGnAL' (Table ). We retrieved normalized gene expression data for the selected probe sets from the 'Genevestigator Digital Northern' tool [] covering more than 1,800 microarrays. U […]

library_books

Genome wide analysis of CCCH zinc finger family in Arabidopsis and rice

2008
BMC Genomics
PMCID: 2267713
PMID: 18221561
DOI: 10.1186/1471-2164-9-44

[…] ool algorithms BLASTP and TBLASTN with various published CCCH proteins as query sequences and with the E-value cutoff set as 1e-005. For Arabidopsis, the databases searched included NCBI [], DATF [], MAtDB [], TAIR [], and TIGR [] and for rice, the databases searched included NCBI [], TIGR [], Rice Genome Database-japonica of the Rice Genome Research Program [] and The International Rice Genome Se […]

library_books

Gender specific selection on codon usage in plant genomes

2007
BMC Genomics
PMCID: 1919372
PMID: 17567911
DOI: 10.1186/1471-2164-8-169

[…] s []. A similar analysis was conducted for male-specific and flower-specific genes in B. napus. The gene functions were determined by comparison to proteins characterized in the A. thaliana database (MATDB)[] with annotation from The Arabidopsis Information Resource (TAIR) and as implemented by the software Classification Superviewer []. […]

library_books

Genome wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa

2005
BMC Evol Biol
PMCID: 1368998
PMID: 16368012
DOI: 10.1186/1471-2148-5-72

[…] e TAIR website using Patmatch. Arabidopsis nucleotide and protein sequences as well as information regarding the gene structure were obtained from the Munich Information Center for Protein Sequences (MIPS) Arabidopsis thaliana Database (MATDB) [], The Institute for Genomic Research (TIGR) Arabidopsis thaliana Database [], and the Arabidopsis thaliana Plant Genome Database (AtPGD) []. To identify m […]

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MAtDB institution(s)
Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Neuherberg, Germany; Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Germany
MAtDB funding source(s)
This work was supported by the GABI and PlaNet projects.

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