transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

Background: Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem. For protein-coding DNA sequences, it is more advantageous in terms of both speed and accuracy to align the amino-acid sequences specified by the DNA sequences rather than the DNA sequences themselves. Many implementations making use of this concept of "translated alignments" are incomplete in the sense that they require the user to manually translate the DNA sequences and to perform the amino-acid alignment. As such, they are not well suited to large-scale automated alignments of large and/or numerous DNA data sets. Results: transAlign is an open-source Perl script that aligns protein-coding DNA sequences via their amino-acid translations to take advantage of the superior multiple-alignment capabilities and speed of an amino-acid alignment. It operates by translating each DNA sequence in...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Olaf R. P. Bininda-Emonds
• Keywords: Amino-acid, Amino-acid Alignment, BMCBI 2005, Dna Sequences