Motivation: Large alignments of ribosomal RNA sequences are maintained at various sites. New sequences are added to these alignments using a combination of manual and automatic methods. We examine the use of profile alignment methods for rRNA alignment and try to optimize the choice of parameters and sequence weights.
Results: Using a large alignment of eukaryotic SSU rRNA sequences as a test case, we empirically compared the performance of various sequence weighting schemes over a range of gap penalties. We developed a new weighting scheme which gives most weight to the sequences in the profile that are most similar to the new sequence. We show that it gives the most accurate alignments when combined with a more traditional sequence weighting scheme.
Availability: The source code of all software is freely available by anonymous ftp from chah.ucc.ie in the directory /home/ftp/pub/emmet,in the compressed file PRNAA.tar:
Contact: emmet@chah.ucc.ie, des@chah.ucc.ie