i am a beginner in bio-bioinformatics and working with whole genome allignment and i need single gene segment out. but i find gaps in some seq and in some not (plz see the attached pic). how to deal with such things? alignment eg
It depends totally on what you want to do with the alignment afterwards. However, recent evidence suggests that you are losing phylogenetic information if applying automated alignment trimming, and I am not sure, manual trimming will do any better, while in addition being arbitrary. Both Maximum-Likelihood and Bayesian inference can deal with gaps, so it is possibly best to leave them in.
hi Michael,thank you, yes my next step of analysis would be phylogenetic tree construction. but when i translate them to proteins, i find incomplete ORF, so in that case is it ok to leave them such way?
What kind of organism is it? Maybe you can translate the sequence to AA first then align these, or use a codon model. But for that to work, you need to be quite sure that you have a good transcript sequence without frame shifts. For the codon model to work, you also need to have the exact start codon. Your sequences seem to be quite similar on the DNA level though (looks like two major groups, and several strains), so you might be able to use the DNA alignment directly.
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Looks like you already have done the alignments.
You can use MEGA or JalView to edit them (within reason).
yes @genomax thanx for your input, this is already alligned by MAFT. and i am using MEGA to edit them.
hi Michael,thank you, yes my next step of analysis would be phylogenetic tree construction. but when i translate them to proteins, i find incomplete ORF, so in that case is it ok to leave them such way?