Sequence.: Difference between revisions
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Multiple sequence alignments: | Multiple sequence alignments: | ||
NonredundantMSA | [[Image:NonredundantMSA.pdf]] | ||
An alignment of a blast search of the NCBI's nonredundant database. Some of the sequences are protein or translated cDNA, but many come from genome annotations, with no functional information. For some organisms, a few variants of the sequence are included. The sources are both prokaryotes and eukaryotes. | |||
(~180 sequences) | |||
[[Image:TopNonredundantMSA.pdf]] | [[Image:TopNonredundantMSA.pdf]] | ||
A realignment of the most similar sequences from above. | |||
(155 sequences) | |||
These two MSAs show that the sequence has been well conserved - some of the residues almost 100% conserved over a wide variety of organisms. I will use these for the phylogenetic tree. However, if you use these to make other inferences, keep in mind that some of these sequences may not code for ssu72 (or anything else)... | |||
[[Image:SwissProtMSA.pdf]] | [[Image:SwissProtMSA.pdf]] | ||
An alignment from a blast search of SwissProt. The data is higher quality and less redundant, and there is functional information for each sequence. Of the 24 sequences, 3 are human ssu72 homologues, and the others are ssu72 from various organisms. | |||
This MSA shows the conserved regions for ssu72. Since these are ssu72 sequences, I think the residues that show up as conserved here are probably important for structure/function. | |||
Revision as of 12:15, 6 June 2009
Multiple sequence alignments:
An alignment of a blast search of the NCBI's nonredundant database. Some of the sequences are protein or translated cDNA, but many come from genome annotations, with no functional information. For some organisms, a few variants of the sequence are included. The sources are both prokaryotes and eukaryotes. (~180 sequences)
A realignment of the most similar sequences from above. (155 sequences)
These two MSAs show that the sequence has been well conserved - some of the residues almost 100% conserved over a wide variety of organisms. I will use these for the phylogenetic tree. However, if you use these to make other inferences, keep in mind that some of these sequences may not code for ssu72 (or anything else)...
An alignment from a blast search of SwissProt. The data is higher quality and less redundant, and there is functional information for each sequence. Of the 24 sequences, 3 are human ssu72 homologues, and the others are ssu72 from various organisms. This MSA shows the conserved regions for ssu72. Since these are ssu72 sequences, I think the residues that show up as conserved here are probably important for structure/function.
