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  • Comparing Transcriptomes and finding common transcript IDs

    Hi,

    I have two transcriptomes, Transcriptome_old and Transcriptome_new both generated using de novo approach at different time point with different lengths. Now I would compare these these transcriptomes and later get the transcript id of transcriptome_recent and the corresponding id of Transcriptome_old which shares common sequence between them. I mean I would like compare the sequences and get the corresponding ids of both old and recent transcriptome. Kindly guide me how to achieve it.

    Thanks in advance

  • #2
    You can BLAT them against each other.

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    • #3
      Originally posted by GenoMax View Post
      You can BLAT them against each other.
      Did you meant BLAST?

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      • #4
        I meant BLAT. Hopefully the transcriptomes are pretty similar.

        Comment


        • #5
          Originally posted by GenoMax View Post
          I meant BLAT. Hopefully the transcriptomes are pretty similar.
          I am trying to install BLAT but somehow it throws error when I use "make" command amd I am currently finding th solution for it. Is there any alternative way to address my question. Kindly guide me

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          • #6
            You could perform a Blast all vs all and then use the output to cluster your sequences with ORTHOMCL. I think it's a better approximation because paralog genes may hinder the searching.

            I hope it helps!

            Comment


            • #7
              Originally posted by dena.dinesh View Post
              I am trying to install BLAT but somehow it throws error when I use "make" command amd I am currently finding th solution for it. Is there any alternative way to address my question. Kindly guide me
              If you are not from a commercial entity you could get the pre-compiled binaries here: http://genome-test.cse.ucsc.edu/~kent/exe/

              You could also try CD-HIT-2D.

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