Sequence.: Difference between revisions
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Multiple sequence alignments: | Multiple sequence alignments: | ||
NonredundantMSA | 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. | ||
NonredundantMSAtop is the alignment repeated without the less similar sequences (mostly without the prokaryotic ones). | NonredundantMSAtop is the alignment repeated without the less similar sequences (mostly without the prokaryotic ones). | ||
These MSAs show that the protein has been well conserved | 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... | ||
[[Image:NonredundantMSA.pdf]] | [[Image:NonredundantMSA.pdf]] | ||
[[Image:TopNonredundantMSA.pdf]] | |||
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. | 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. | ||
Since these are ssu72 sequences, this is the more useful MSA for noting conserved regions. | Since these are ssu72 sequences, this is the more useful MSA for noting conserved regions. | ||
[[Image:SwissProtMSA.pdf]] | |||
Revision as of 12:03, 6 June 2009
Multiple sequence alignments:
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. NonredundantMSAtop is the alignment repeated without the less similar sequences (mostly without the prokaryotic ones). 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...
File:NonredundantMSA.pdf File:TopNonredundantMSA.pdf
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.
Since these are ssu72 sequences, this is the more useful MSA for noting conserved regions.
