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A probabilistic model of local sequence alignment that simplifies statistical significance estimation.

Sean R Eddy

PLoS computational biology 4 (5), e1000069 (May 2008)

info:pmid/18516236 | info:doi/10.1371/journal.pcbi.1000069

Posted by eckart_bindewald and 2 others to Alignment statistical hmm on Thu Jun 05 2008 at 19:46 UTC | info | related

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Mulan Multiplesequence local alignment and visualization for studying function and evolution

Ivan Ovcharenko et al.

Genome Research 15 (1), 184-94 (01 Jan 2005)

info:doi/10.1101/gr.3007205

Posted by eckart_bindewald and 1 other to Alignment visualization genome on Fri Apr 11 2008 at 12:18 UTC | info | related

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.

Elfar Torarinsson et al.

Genome Research 16 (7), 885-9 (01 Jul 2006)

info:doi/10.1101/gr.5226606

Posted by eckart_bindewald and 3 others to conserved noncoding Alignment prediction RNA on Fri Apr 11 2008 at 12:18 UTC | info | related

RNAs everywhere: genome-wide annotation of structured RNAs.

Rolf Backofen et al.

J Exp Zoolog B Mol Dev Evol 308B (1), 1-25 (14 Dec 2006)

info:pmid/17171697 | info:doi/10.1002/jez.b.21130

Posted by eckart_bindewald and 1 other to conserved noncoding Alignment prediction RNA on Fri Apr 11 2008 at 12:18 UTC | info | related

Noncoding RNA gene detection using comparative sequence analysis.

E Rivas and S R Eddy

BMC Bioinformatics 2, 8 (2001)

info:pmid/11801179

Posted by eckart_bindewald and 3 others to secondary_structure noncoding Alignment prediction RNA on Fri Apr 11 2008 at 12:18 UTC | info | related

Multiple structural alignment and clustering of RNA sequences.

Bioinformatics 23 (8), 926 (2007)

info:doi/10.1093/bioinformatics/btm049

Posted by eckart_bindewald to secondary_structure secondary Alignment RNA structure on Fri Apr 11 2008 at 12:18 UTC | info | related

Minimus: a fast, lightweight genome assembler

Minimus a fast lightweight genome assembler

Daniel D Sommer et al.

BMC Bioinformatics 8 (1), 64 (26 Feb 2007)

info:pmid/17324286 | info:doi/10.1186/1471-2105-8-64

Posted by eckart_bindewald and 2 others to Alignment assembly genome on Fri Apr 11 2008 at 12:18 UTC | info | related

Stem kernels for RNA sequence analyses.

Yasubumi Sakakibara et al.

Journal of bioinformatics and computational biology 5 (5), 1103-22 (Oct 2007)

info:pmid/17933013

Posted by eckart_bindewald to noncoding Alignment prediction RNA sequence on Fri Apr 11 2008 at 12:18 UTC | info | related

Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.

R Satija, L Pachter, and J Hein

Bioinformatics (Oxford, England) 24 (10), btn104v1 (18 Mar 2008)

info:pmid/18353788 | info:doi/10.1093/bioinformatics/btn104

Posted by eckart_bindewald and 5 others with 1 comment to Alignment statistical elements regulatory on Fri Apr 11 2008 at 12:18 UTC | info | related

Combining phylogenetic data with co-regulated genes to identify regulatory motifs.

Ting Wang and Gary D. Stormo

Bioinformatics 19 (18), 2369-80 (12 Dec 2003)

info:doi/10.1093/bioinformatics/btg329

Posted by eckart_bindewald to Alignment ortholog Phylogenetic motif discovery on Fri Apr 11 2008 at 12:18 UTC | info | related

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