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» Benchmarking tools for the alignment of functional noncoding...
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BMCBI
2004
85views more  BMCBI 2004»
13 years 4 months ago
Benchmarking tools for the alignment of functional noncoding DNA
Daniel A. Pollard, Casey M. Bergman, Jens Stoye, S...
BMCBI
2006
137views more  BMCBI 2006»
13 years 4 months ago
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
Background: Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch...
Rahul Siddharthan
BMCBI
2010
118views more  BMCBI 2010»
13 years 4 months ago
Towards realistic benchmarks for multiple alignments of non-coding sequences
Background: With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the mo...
Jaebum Kim, Saurabh Sinha
NAR
2010
107views more  NAR 2010»
12 years 11 months ago
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attun...
Satish Chikkagoudar, Dennis R. Livesay, Usman Rosh...
BMCBI
2010
138views more  BMCBI 2010»
13 years 4 months ago
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
Background: While most multiple sequence alignment programs expect that all or most of their input is known to be homologous, and penalise insertions and deletions, this is not a ...
Gayathri Jayaraman, Rahul Siddharthan