Comparing Genome Derived And Cdna Derived Protein Sequences

Question

[Woa]

I've two sets of protein sequences for a particular organism for which the genome sequence is available to us.

One of the protein sets is derived from comparing the genome with all the proteins of a related organism using a protein-genome alignment program.

The second protein set was derived from a translated cDNA library from the same organism.

I wish to find out the equivalent pair of proteins(supposedly almost identical) from these two sets.

Can anybody suggest any good method for this? Can I use 'reciprocal blast best hits' method?

Thanks in advance

WoA

[Woa]

However things went not so good. Many of the cDNA proteins were fragments and they are yielding erroneous results. Can anybody suggest any alternative way to bypass the problem?

Answer 1

[Larry_Parnell]

Yes, the reciprocal or mutual best BLASTP hit approach will work. It may miss a couple of pairings, but will find in excess of 99%, in my opinion.

Answer 2

[h.mon]

Map both your predicted proteins and the cDNA against the genome, the overlaps will give you what you want. Spaln perform both alignments and it is quite fast, you can probably run it on your personal computer for your datasets.

[h.mon]

oh crap, sorry I am posting to a very old question. shame on me.