Useful resources

Software / applications developed by OmicsLab

A web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. Compared with available GO analysis tools, GOEAST has the following unique features:
  • GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats.
  • GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy.
  • GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis.
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    Integrative Short Reads NAvigator (ISRNA) is an online toolkit for searching, analyzing and visualizing short sequence reads data generated by high-throughput sequencing technologies. Major functions of the toolkit include:
  • Fast and accurate mapping of short reads to a given genome.
  • General bioinformatic analysis of the input sequence reads, such as nucleotide composition, length distribution, sequence annotation, miRNA identification, RNA secondary structure prediction, short read cluster discovery, etc.
  • Versatile searching functions for curation of sequence reads, including searching the dataset by certain sequence or sequence motifs, by known miRNA names, by reads counts, by genomic location, and by the name or annotation of adjacent protein coding genes.
  • A genome browser for visualizing the distribution of sequencing reads and corresponding genes.
  • Multiple datasets management and cross-datasets comparison.
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    PsRobot is a web-based analysis toolbox for plant small RNAs and their targets. It was developed for the identification and functional analysis of user-uploaded small RNAs and their targets. The functions of psRobot include:
  • Genomic location of uploaded small RNAs
  • Relationship of small RNAs with repeat-seqeunces and the repeat types
  • Expression data of small RNAs in key small RNA biogenesis related protein complexes
  • Folding of small RNA precursor sequences with stem-loop shaped secondary structures
  • Putative targets of uploaded small RNAs
  • Conservation status of small RNAs and target sites in Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, Zea mays, Carica papaya, Brachipodium distachyon, Populus trichocarpa and Vitis vinifera
  • Cleavage information of target mRNAs in degradome data
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    Thellungiella salsuginea genome
    Here are the links to download the draft sequence of the T. salsuginea genome, assembled based on ∼134-fold coverage to seven chromosomes with a coding capacity of at least 28,457 genes. For detailed information, please check Wu et. al., PNAS, 2012.
    Download all files below as an RAR archive
    Thellungiella salsuginea genome release 1.0, chromosomes   Download
    Thellungiella salsuginea genome release 1.0, gene GFF file   Download
    Thellungiella salsuginea genome release 1.0, gene GO annotations   Download
    Thellungiella salsuginea genome release 1.0, mRNAs   Download
    Thellungiella salsuginea genome release 1.0, CDS   Download
    Thellungiella salsuginea genome release 1.0, proteins   Download
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