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Old 03-31-2015, 04:14 AM   #1
dena.dinesh
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Default 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
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Old 03-31-2015, 04:33 AM   #2
GenoMax
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You can BLAT them against each other.
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Old 03-31-2015, 04:43 AM   #3
dena.dinesh
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Quote:
Originally Posted by GenoMax View Post
You can BLAT them against each other.
Did you meant BLAST?
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Old 03-31-2015, 04:46 AM   #4
GenoMax
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I meant BLAT. Hopefully the transcriptomes are pretty similar.
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Old 03-31-2015, 05:22 AM   #5
dena.dinesh
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Quote:
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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Old 03-31-2015, 05:22 AM   #6
diego diaz
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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!
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Old 03-31-2015, 05:29 AM   #7
GenoMax
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Quote:
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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