Background: In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses an...
Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables...
Joseph N. Zadeh, Conrad Steenberg, Justin S. Bois,...
Motivation: Non-coding RNAs (ncRNAs)--functional RNA molecules not coding for proteins--are grouped into hundreds of families of homologs. To find new members of an ncRNA gene fam...
Background: Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selec...