Which software can be used for this issue?
Is it important to remove introns from DNA sequence when we want to establish a phylogenetic tree from several genes with a Maximum Likelihood inference ? What could happen if we don't and so let the introns included ?
Thanks you for your attention
Hi,
If you are using Genbank there should be mRNA records for your gene of interest. These should not have introns, but might include some 5' and 3' UTR. It is best not to include introns in a phylogenetic analysis because they ar usually not under the same selective pressure as the gene product during evolution and therefore might diverge at a different rate.
If you look at the mRNA sequence record (example http://www.ncbi.nlm.nih.gov/nuccore/JF751028.1) you see a section FEATURES. Here the CDS is the coding sequence and will give you the sequence that codes for protein. That section of the sequence is what you would use for analysis usually, unless of course you are interested in UTRs...
I hope this helps,
-Anna
Hi,
If you are using Genbank there should be mRNA records for your gene of interest. These should not have introns, but might include some 5' and 3' UTR. It is best not to include introns in a phylogenetic analysis because they ar usually not under the same selective pressure as the gene product during evolution and therefore might diverge at a different rate.
If you look at the mRNA sequence record (example http://www.ncbi.nlm.nih.gov/nuccore/JF751028.1) you see a section FEATURES. Here the CDS is the coding sequence and will give you the sequence that codes for protein. That section of the sequence is what you would use for analysis usually, unless of course you are interested in UTRs...
I hope this helps,
-Anna
Following Anna's comment, I would suggest to use these mRNA records and align them to your own sequences. You sould see large gaps where the introns are in the reference sequences from Genbank. Make sure to identify the boundaries correctly (introns have specific starts and end sequences) and remoe the introns from your sequences by hand (e.g in Bioedit).
Martin
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