Blastn x megablast - homologous genes

clarissaboschi · 02-01-2017, 09:22 AM

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 · 02-01-2017, 09:58 AM

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 · 02-01-2017, 01:21 PM

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 · 02-01-2017, 03:00 PM

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

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02-01-2017, 09:22 AM	#1
clarissaboschi Member Location: US Join Date: Apr 2010 Posts: 63	Blastn x megablast - homologous genes 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 Last edited by clarissaboschi; 02-01-2017 at 01:31 PM.

02-01-2017, 09:58 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	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

02-01-2017, 01:21 PM	#3
clarissaboschi Member Location: US Join Date: Apr 2010 Posts: 63	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.

02-01-2017, 03:00 PM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Sorry, you're right about the protein vs nucleotide focus.