Hi Xy Ma, Generally speaking there should be no need to customize the alignment parameters for chloroplast genomes. However, there are two items of concern: first is that chloroplasts contain multi-copy gene families. progressiveMauve will calculate a positional homology alignment, meaning that only the copies which are positionally conserved (as determined by the alignment algorithm) will become aligned to each other. Depending on what you plan to do next this behavior may or may not be desirable.
Second, chloroplasts as a whole are fairly diverse and the sequence identity in the whole group is probably too low for alignment with progressiveMauve, which has difficulty aligning sequences below about 60% nucleotide identity (though lower identity can be handled in some cases). But if you're planning to focus in on specific clades it should be just fine. Best, -Aaron On Mon, 2014-04-21 at 16:25 +1000, usermxy wrote: > > > Dear Sir/Miss, > > > > > > I want to do the chloroplast genome alignment by Progressive Mauve. > > > > How do I choose the related parameters (such as match seed weight， > > minimum LCB score…) in advance? > > > > Is the default setting OK? No matter the species number and the > > diversity among them? > > > > How can I identify the best alignment results or what is the best > > alignment results? > > > > Dose it make sense that I do the alignment with different parameters > > and compare the different results? If so，what should I do? > > > > > > Thank you very much. > > > > Best Regards, > > > > > > Dr. Xy Ma > > > > Guangzhou University of Chinese Medicinesprut > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Is your legacy SCM system holding you back? Join Perforce May 7 to find out: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
