Question: Blast W/ G:T Pairing?
1
gravatar for Sequencegeek
8.7 years ago by
Sequencegeek740
UCLA
Sequencegeek740 wrote:

I'm using BLAST for a part of my pipeline and need to change my pipeline to allow G/U matching. My google foo isn't getting me very far. Does anyone know if there is a similar version of BLAST with this capability?

Thanks

mapping blast • 1.2k views
ADD COMMENTlink written 8.7 years ago by Sequencegeek740
2
gravatar for Larry_Parnell
8.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

If you want to use BLASTN, it would be best to do so locally so that you can employ your own scoring matrix. If you cannot find a scoring matrix which allows G:U or G:T pairing, you'll have to build it. You'll want to change M and N, where the M parameter sets the reward score for a pair of matching residues and N sets the penalty score for mismatching residues. Typically M=5 and N=-4. If a G:T pair is weaker than G:C, maybe it should have a score of 1, midway between M of 5 and N of -4.

For more on scoring matrices, see this.

ADD COMMENTlink written 8.7 years ago by Larry_Parnell16k
1
gravatar for Manu Prestat
8.7 years ago by
Manu Prestat4.0k
Lyon, France
Manu Prestat4.0k wrote:

I don't know if it fast enough for you, but locARNA allows this kind of matching.

ADD COMMENTlink written 8.7 years ago by Manu Prestat4.0k
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