Comparing Transcriptomes and finding common transcript IDs

[dena.dinesh]

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

[GenoMax]

You can BLAT them against each other.

[dena.dinesh]

You can BLAT them against each other.

Did you meant BLAST?

[GenoMax]

I meant BLAT. Hopefully the transcriptomes are pretty similar.

[dena.dinesh]

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

[diego diaz]

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!

[GenoMax]

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.