Multiple sequence alignments of partially coding nucleic acid sequences |
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| Authors: | Roman R Stocsits Ivo L Hofacker Claudia Fried and Peter F Stadler |
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| Institution: | (1) Interdisciplinary Centre for Bioinformatics, University of Leipzig, Haertelstra?e 16-18, D-04107 Leipzig, Germany;(2) Institute for Theoretical Chemistry, University of Vienna, W?hringerstra?e 17, A-1090 Wien, Austria;(3) Bioinformatics Group, Department of Computer Science, University of Leipzig, Haertelstra?e 16-18, D-04107 Leipzig, Germany;(4) Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA |
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| Abstract: | Background High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic
sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein
sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when
aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On
the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding
parts. Examples are, in particular, RNA virus genomes. |
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