Blastn x megablast - homologous genes

[clarissaboschi]

I have a list of nucleotide sequences (genes) and I would like to Blast against a list of nucleotide sequences from other species to check potential homologous sequences (orthologs and paralogs).

Which blast is best for it? Blastn or Megablast?

My smallest sequence has 12 nucleotides, and the largest has 16,000.

Thanks

[maubp]

This might be worth reading:

Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
or How To Use Sequence and Structure Information To Predict Protein
Function. PLoS Comput Biol 4(10): e1000160.
http://dx.doi.org/10.1371/journal.pcbi.1000160

[clarissaboschi]

maubp it is a good paper, but did not help me, because is more focus in protein sequence analysis. I know is better to use protein sequences for it, but I need to use nucleotide sequences.

I am wondering if in my case is better to use dc-megablast because I am searching sequences for cross-species comparisons.

[maubp]

Sorry, you're right about the protein vs nucleotide focus.