Abstract
BackgroundMultiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated.ResultsWe evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment.ConclusionMULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.
Highlights
Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes
As a byproduct of our procedure, we predict many novel instances of known noncoding RNA (ncRNA) families that are suggested by the alignment
We use the software package Infernal to analyze each of the sequences aligned by MULTIZ to the human ncRNA
Summary
Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. The accuracy of whole-genome multiple alignments, in noncoding regions, has not been thoroughly evaluated. In this time when so many genome sequences are reaching completion, alignments of multiple whole genomes are of great value to biologists, since enlightening evolutionary information is encoded in the conservation and variation across species. We use alignments of noncoding RNA (ncRNA) as a test of the accuracy of multiple alignment of genomic regions that are difficult to align This is a rather challenging test, as many functional RNAs exhibit weak primary sequence conservation [5]. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment We return to this topic in the Discussion section
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