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A cross-platform and cross-species desktop application for genome sequence visualization and navigation.
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Comparative Resources
NCBI's system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
A collection of pairwise comparisons between 17 640 eukaryotic whole genomes including Arabidopsis thaliana, useful for the identification of orthologs and differentiation between inparalogs and outparalogs.
Contains comparisons of Arabidopsis, rice,and poplarmany plant species.
Access point for plant comparative genomics centralizing genomic data produced by different genome sequencing initiatives. PLAZA integrates plant sequence data and comparative genomics methods and provides an online platform allowing to perform evolutionary analyses and data mining within the green plant lineage (Viridiplantae).
A comparative genomics platform designed to allow easy access to genomic data from any organism and provide analysis tools for finding and comparing homologous sequences from multiple genomic regions.
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A genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana.
The Arabidopsis thaliana promoter binding element database, an aid to find binding elements and check data against the primary literature.
DATF: Database of Arabidopsis Transcription Factors
The Database of Arabidopsis Transcription Factors (DATF) contains known and predicted Arabidopsis transcription factors with sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and Nuclear Location SignalsBecause of the PI's retirement, this database may be switched of any time after July 1st 2023.
This resource can be used to query co-expression data, GO and cis-regulatory elements annotations, submit user-defined gene sets for motif analysis for Arabidopsis and provides an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis.
DoOP: Databases of Orthologous Promoters
A database containing orthologous clusters of promoters from Homo sapiens, Arabidopsis thaliana and other organisms.(non-https server)
Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
Database with annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start sites (TSS) from various plant species.
Database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only.
PlantTFDB: Plant Transcription Factor Database
An integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of a large number of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri.
Database that provides transcription start sites (TSS) and other structural information for Arabidopsis and rice thaliana, Oryza sativa, and Physcomitrella patens and poplar promoters.PRI-CAT
Plant Research International ChIP-seq analysis tool is a web-based workflow tool for the management and analysis of ChIP-seq experiments. Users can directly submit their sequencing data to PRI-CAT for automated analysis.
Database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Commercial site.
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NCBI's Entrez Databases -retrieve sequences and other data, including literature, from PubMed.
UniProt reflects a merge of 3 databases, SwissProt,PIR and TrEMBL and replaces these databases. Search UniProtKB, a database of curated protein sequences (formerly Swiss-Prot).
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micro-RNA database for micro-RNA sequences from more than 270 species, including A. thaliana.
The non-coding RNA sequence database, a comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms .
BLAST servers
Search against all public Arabidopsis sequences, several subsets of them, or all higher plant sequences from GenBank. These datasets can be downloaded.
BLAST server at NCBI
BLAST manual and user guide from NCBI
