Blast expressed tag sequence using mRNA or genomic sequence - (Jul/09/2008 )
Hi everybody,
I am using GENE SCAN to predict novel gene. Then, senior tols me have to blast for any EST...but unfortunately she is no familiar with this..
The predicted gene model showed 3 types information, ie., protein, mRNA and genomic DNA. In my opinion, mRNA sequence shld be used to blast for EST. But I didn't get any match EST, except in non-human. So, I try blast using genomic DNA, and get a lot of hits.
I dunno what puporse to blast EST since the predicted model provided mRNA sequence. 
Another question is how to look for protein similarity of predicated model? using mRNA sequence? or direct predicted Protein sequence?
Thank you...
-mes08-
QUOTE (mes08 @ Jul 9 2008, 10:30 PM)
Hi everybody,
I am using GENE SCAN to predict novel gene. Then, senior tols me have to blast for any EST...but unfortunately she is no familiar with this..
The predicted gene model showed 3 types information, ie., protein, mRNA and genomic DNA. In my opinion, mRNA sequence shld be used to blast for EST. But I didn't get any match EST, except in non-human. So, I try blast using genomic DNA, and get a lot of hits.
I dunno what puporse to blast EST since the predicted model provided mRNA sequence.
Another question is how to look for protein similarity of predicated model? using mRNA sequence? or direct predicted Protein sequence?
Thank you...
I am using GENE SCAN to predict novel gene. Then, senior tols me have to blast for any EST...but unfortunately she is no familiar with this..
The predicted gene model showed 3 types information, ie., protein, mRNA and genomic DNA. In my opinion, mRNA sequence shld be used to blast for EST. But I didn't get any match EST, except in non-human. So, I try blast using genomic DNA, and get a lot of hits.
I dunno what puporse to blast EST since the predicted model provided mRNA sequence.
Another question is how to look for protein similarity of predicated model? using mRNA sequence? or direct predicted Protein sequence?
Thank you...
In most databases when they give you the mRNA sequence it is just a prediction based on a computer program. Most times it is correct, but there are cases where genes may not be expressed at all, or they are transcribed (and then translated) differently from what one would predict. That is why it is helpful to blast an EST database (EST means expressed sequence tag) which comes from actual expressed sequences so you know that the mRNA prediction is true.
-smu2-