[Bioperl-l] (no subject)

[Dave Messina]

Okay, let me see if I've got this straight: you want to do Ka/Ks on just the
subsequences of the cDNAs that match the HMMer domain?

e.g.
1) You have a cDNA sequence. Let's call it Xn.
2) Xn is 300 nucleotides in length.
3) You translate Xn into protein Xp.
4) You use HMMer to search Xp against Pfam.
5) HMMer tells you that Xp has, for example, an SH2 domain from residue 30
to residue 51.
6) Likewise, let's say two additional proteins Yp and Zp have the same SH2
domain.

You want to:
7) Determine which nucleotides in Xn correspond to amino acids 30-51 in Xp.
8) Extract just those nucleotides (and also the nucleotides in Yn and Zn
corresponding to their SH2 domain hits).
9) Align those nucleotide sequences.
10) Give the resulting multiple alignment to PAML and calculate the Ka/Ks
ratios.

Is that correct?
Is it steps 7 and 8 that you are trying to solve?


Dave