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  • mirTools for microRNA profiling and discovery based on high-throughput sequencing

    mirTools: a web server for microRNA profiling and discovery based on high-throughput sequencing

    Although deep-sequencing schemes can be applied to unbiased, quantitive and in-depth investigation of the small RNA transcriptome that has been previously possible, they present substantial informatics challenges for lack of efficient and flexible tools to handle and analysis a huge scale of short sequences. Therefore, a comprehensive web server mirTools was developed to allow researchers to comprehensive characterizes the small RNA transcriptome. With the aid of mirTools, it can:
    1) Align the large-scale short reads to the reference genome and exhibit the length distribution;
    2) Classify of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences;
    3) Provide detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag;
    4) Discovery of the novel miRNAs that have not been characterized before from the large-scale short reads;
    5) Identify of the differentially expressed miRNAs between samples according to different count strategies, such as total read tag counts and the most abundant tag of specific miRNA.

    Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Research. 2010

    mirTools can be available at http://centre.bioinformatics.zj.cn/mirtools/.
    Last edited by zhuerle; 06-20-2010, 01:03 AM. Reason: add cite information

  • #2
    There is a novel datbase/platform deepBase, which were developed to map, store, retrieve, annotate, integrate and visualize deep sequencing-derived small RNAs, and facilitate transcriptomic research and the discovery of novel ncRNAs.

    about 2000 microRNA(miRNA) candidates were identified from deep sequencing data from different technology platforms, tissues and cell lines from seven organisms in deepBase.

    deepBase is available at: http://deepbase.sysu.edu.cn/

    deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., December 4, 2009




    more details see: http://seqanswers.com/forums/showthread.php?t=3395

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    • #3
      The two tools are the same powerfull O(∩_∩)O~
      Last edited by houhuabin; 12-17-2009, 08:21 PM.

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      • #4
        mirTools welcome any comment, suggestion or question, which will be an important step for enhancing it power and our future update.

        Please do not hesitate to contact us!

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        • #5
          A list of Web-Based Tools for MicroRNA Analysis from Deep Sequencing Data can be see from miRNA Blog (http://mirnablog.com/web-based-tools...quencing-data/)

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          • #6
            Dear mirTools users,

            Recently, the computational efficiency of mirTools has been enhanced, which is equipped with four Quad-Core AMD processors (2.2 GHz each) and 32 GB of RAM. Now, a typical run may take one-two hours to finish, depending on the data size, reference genome size and queuing jobs.

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            • #7
              Dear Jinyu, The tool is wonderful. Do you think to add other reference genomes? I am particularly interested in Sorghum bicolor. Regards

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              • #8
                Hello crisant,

                Thank you for your interests in mirTools. Currently, mirTools only contain 15 reference genome which is completely finished. mirTools depends on a number of reference data to annotate the small RNA transcriptome, such as miRBase, Rfam, The RepeatMasker of reference genome.

                Now, we are developing addtional pipeline to annotate the the small RNA transcriptome from whose reference genome is not completely finished or just has the EST data. The web interface is under serious developing and the pipeline will come soon. If your project is emergent, you can contact me ([email protected]) or Erle Zhu ([email protected]). We will run your data locally and send the corresponding result to your soon.

                Best,

                Jinyu Wu

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                • #9
                  Hello

                  mirTools has been updated recently, which can allow users to analyze the experiment with replicate(s). Welcome to try this function at http://centre.bioinformatics.zj.cn/mirtools/group.php.

                  Best,

                  Erle Zhu

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                  • #10
                    is mirTools available for download, so that we could analyse data locally, add in our own reference genomes, etc?

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                    • #11
                      Hello blackgore

                      Sorry for response too later. The mirTools web server was developed toward a fully automated and easy to use web service suitable for small RNA transcriptome analyses. It dose not allow to be download.

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                      • #12
                        Does mirTools support SOLiD reads (colour space data)?

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                        • #13
                          Hello teshome,
                          Thank you for your interests in mirTools. Currently, mirTools does not support SoLID color space.

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                          • #14
                            Hello,
                            mirTools has been published in NAR. http://nar.oxfordjournals.org/cgi/content/full/gkq393
                            Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Research. 2010
                            Last edited by zhuerle; 06-20-2010, 01:13 AM. Reason: edit

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                            • #15
                              Hi,

                              I just wondering whether mirTools got the pipeline of microRNA deals for Illumina data?
                              Thanks for sharing.

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