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| Multiple sequence alignments:
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| NonredundantMSA is an alignment a blast search of the nonredundant database. Some of these sequences are cDNA/protein, but many are genome annotations with unknown function. For some organisms, a few variants of the sequence are included, so it's redundant in that sense. This has both prokaryotic and eukaryotic sources.
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| NonredundantMSAtop is the alignment repeated without the less similar sequences (mostly without the prokaryotic ones).
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| These MSAs show that the protein has been well conserved. They also show that there are some residues which have been almost 100% conserved in ~180 sequences. I will use these for my tree, but if you use these to make other inferences, keep in mind that some of these genes may not code for ssu72...
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| [[Image:NonredundantMSA.pdf]]
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| [[Image:TopNonredundantMSA.pdf]]
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| SwissProtMSA is an alignment from a blast search of SwissProt, so there is functional information for each sequence, and the data is higher quality. There are 24 sequences: 21 ssu72 from a variety of different organisms and 3 ssu72 homologues from human.
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| Since these are ssu72 sequences, this is the more useful MSA for noting conserved regions.
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| [[Image:SwissProtMSA.pdf]]
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