ABSTRACT: BACKGROUND: Multiple alignment of DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. RESULTS: We evaluate the alignment accuracy of certain noncoding regions using ncRNA alignments from Rfam as a reference. We inspect the MULTIZ alignments 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 ncRNA elements that are suggested by the alignment. CONCLUSIONS: MULTIZ does a fairly accurate job of aligning 17 vertebrate genomes in these regions. However, our experiments indicate that better alignments exist in some regions.
BMC Bioinformatics 2007;8:417
Rfamのnoncording RNAのアラインメントを利用して、特定のノンコーディング領域の正確性を評価した。Rfamのseed alignmentに含まれる全てのヒトの配列を利用して、UCSCゲノムブラウザから得たMULTIZ-17 vertebrate alignmentを調査した。特に、ヒトnoncording RNA elementに対して、chimericなアラインメントとpartialなアラインメントの例を638個見つけて、それらのうち少なくとも225個は簡単な方法で改善できた。