PairWise and SearchWise: Finding the Optimal Alignment in a Simultaneous Comparison of a Protein Profile against All DNA Translation Frames

• DOI: 10.1093/nar/24.14.2730
• Publication Date: 2002-07-26T18:30:20Z
• Authors: E. Birney; J. D. Thompson; T. J. Gibson
• Keywords: Alignment-free sequence analysis; Multiple sequence alignment; Structural alignment; Translational frameshift

DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal translation. Frameshifts frequently confound computational activities involving homologous sequences, database searches inferences on structure, function phylogeny made from multiple alignments. A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix one more aligned sequences) against the three of strand, allowing frameshifting. The has been incorporated into new package, WiseTools, comparison biological sequences. compared either sequence. program PairWise may used interactively any two inputs. SearchWise perform combinations through databases by Routine application programs revealed set entries with frameshifts caused determination.