Annotation Database
Search
Gene Name Search
Locus Search
Sequence Search
HMM Search
Arabidopsis Links
BAC Tiling Path
Download Sequences
|
The TIGR Arabidopsis thaliana Genome Annotation Database
The A. thaliana genome project is going strong and this page will be updated
as often as possible. When complete, the database will contain every
sequence derived from AGI sequencing projects for the entire genome, annotated
to a uniform standard.
The sequences shown here are from all AGI labs, including TIGR.
Initial annotation for these sequences, where available, is currently being
displayed while we are trying to bring the analysis and annotation up to
the format and standard as performed for TIGR-generated sequences.
A. thaliana annotation data can be accessed through the following features:
Gene Name Search
Text search of the putative identifications in the Gene Identification Table.
Clone Search
Obtain a gene report for a specific clone name.
Locus Search Obtain a report on a predicted coding region by locus number.
BAC Tiling Path
Browse the chromosomes or retrieve a table of clones sorted by chromosome
RNA Gene Table A listing of the transfer RNAs.
Sequence Search Provides searching of nucleotide or peptide sequences against predicted coding regions or the entire genome.
HMM Search Supports searches of protein sequence against a database of hidden Markov models (HMMs) based upon protein families.
Download Sequences FTP access to the entire genome sequence and predicted coding regions.
Additional Arabidopsis thaliana resources:
The Program to Assemble Spliced Alignments (PASA) and associated annotation pipeline was developed and employed towards the improvement of the Arabidopsis genome annotation by incorporating full-length cDNAs and ESTs into gene structures.
Segmental duplications in the Arabidopsis genome with links to duplicated genes.
Tandem gene duplications in the Arabidopsis genome. Computationally identified sets of tandemly duplicated genes in the Arabidopsis genome.
Disease resistance genes identified in Arabidopsis by their domain signatures (mainly describing the NBS-LRR class of disease resistance genes.)
> 1000 Splicing Variations in Arabidopsis were annotated during the incorporation of the currently available EST and full-length cDNA sequences into the Arabidopsis gene structure annotation.
Non-consensus Splice Sites in Arabidopsis based on high quality transcript sequence alignments.
Missing Genes in the Arabidopsis genome.
Genes Classified by Physical Evidence Support. Retrieve gene lists based on user-defined search criteria including matches to proteins and ESTs, or lack thereof.
TIGR's Annotation routine A description on the analysis and annotation performed on the Arabidopsis genomic sequence.
Plan for annotation of sequence from all AGI labs:
- Establish a centralized database for Arabidopsis annotation: ATH1
- Load all available sequence and initial annotation from AGI groups into ATH1.
- Analyze and annotate the sequence to the level currently performed at TIGR.
- Periodically update annotation when new data or software tools are available.
- Present the annotation to the research community
Arabidopsis Comments/Questions
|
