Comparative tramnscriptome analyses and homologous genes

Question

[anagreh_l]

If I have two transcriptomes of a closely related speceis, these two transcriptomes were mapped and annotated, how can I find the transcripts of homologous genes? which software is the best?

Answer 1

[theobroma22]

Use a pair wise or multiple sequence alignment tool, like Blast-2. For large datasets like what you have, use the stand alone Blast+ which you can download from NCBI. First read the manual before downloading/installing, and keep it close to you at all times. It's quite efficient.