Timeline for What is a good multiple alignment of large genome sequences when working with limited hardware?
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| Mar 20, 2017 at 10:29 | history | edited | CommunityBot |
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| Jan 21, 2017 at 9:18 | comment | added | Gigiux | I think I understood why whole alignment is not good as such for inter-species comparison: regions of homology can be dispersed in different parts of the genomes thus there is no co-linearity between sequences. I have found Mauve an excellent tool for inter-species alignments. | |
| Nov 29, 2016 at 13:22 | comment | added | terdon | @Gigiux sorry, for some reason I never saw this comment. The alignment you need depends on the question you want to answer. Yes, sometimes whole genome alignments are useful. Often, however, they are not and you are only interested in specific areas. I can't help you choose unless you explain exactly what you are trying to do. | |
| Nov 3, 2016 at 23:21 | comment | added | Gigiux | The issue of aligning long sequences came out already somewhere else (actually from the developer of muscle); what is such issue? If I have related species (in this case the members of the Mtb complex) doesn't it make sense to align the whole genome and see where differences in genome (especially indels) arise? Isn't this the reason of being of the Whole Genome Sequencing research? | |
| Nov 1, 2016 at 14:10 | history | answered | terdon | CC BY-SA 3.0 |