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  • Identification and grouping of ortholog protein from a set of prokaryotic genomes

    Hi everyone.

    In the frame of a project of comparative genomics, I have right now a set of about 30 whole-genome sequences of bacteria, of about 3-4 Gb size, and need to retrieve orthologous groups of proteins. The idea is to identify common and specific proteomes.

    A former bioinformatician used to use CD-HIT to do so, but I also heard about OrthoMCL.

    Do you know about other "non bioinformatician-friendly" software or bioinformatic tool easy to use?

    I'm not bioinformatician but I'm starting now to introduce in the world of bioinformatics: RSudio, R/Bioconductor, Python… I'm really far by now of dominate all that, but if someone can give me any advice concerning my problem, it will be really appreciated.

    Also, if you know someone experienced in this kind of analysis willing to open a formal collaboration, please, also let me know.

    Thank you in advance!!

  • #2
    I have had good experience with proteinortho (https://www.bioinf.uni-leipzig.de/So.../proteinortho/)
    Personally, I think it is one of the "easy to use" tools you're looking for

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