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This section presents information on tools used for genome annotation, sequence analysis, and sites for data retrieval.
Links need reviewing. Appearance on the list this page does not imply endorsement by TAIR.
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Codon usage tables for many organisms, including Arabidopsis thaliana, from the Kazusa Institute.
AtGDB GeneSeqer webserver for predicting splice junctions in Arabidopsis sequences. Includes a tutorial on how to use the tool.
Family of gene prediction programs provided by the Bioinformatics Group at the Georgia Institute of Technology.
Plant promoter identification
Wise2 compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
Software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence.
MIT's new webserver for GeneScanGenScan. GeneScan GenScan is used to predict the location and intron/exon boundaries in a genomic sequence. Select Arabidopsis as the organism of choice for finding Arabidopsis genes in a genomic sequence.
Predictions of Arabidopsis splice sites from CBSDTU.
Prediction software for Arabidopsis translation starts from CBS.
Search splice sites, protein coding exons and gene models construction, promoter and poly-A signalsDTU.
Software Downloads
Generic Model Organism Database (GMOD) Pages at SourceforgeGitHub
Everything you need to set up a MOD and annotate a genome- all open source software.
The place to find and build open source software
Open source software downloads and open development environment for bioinformatics software.
Multiple Sequence Alignment Tools
Compares overall sequence similarity of multiple sequences.
MEME (Multiple EM for Motif Elicitation)
Analyzes your sequences for similarities among them and produces a description (motif) for each pattern it discovers.
Finds conserved blocks in a group of two or more unaligned protein sequences.
Highlights conserved residues of the resulting multiple sequence alignment.
CINEMA (Colour INteractive Editor for Multiple Alignments)
Editing tool that allows the user to manipulate the alignment.
Aligns DNA or protein sequences and graphically displays the results. Accepts AGI codes as input as well as unaligned or aligned sequences.
Calculates and displays trees based on alignment data (accepts several different input formats)
Whole genome pairwise and multiple alignment editor.
Comprehensive Sequence Analysis Resources
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List of bioinformatic tools and resources
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A cross-platform and cross-species desktop application for genome sequence visualization and navigation.
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Comparative Resources
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