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Items: 1 to 20 of 128

1.

Semiautomated improvement of RNA alignments.

Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J.

RNA. 2007 Nov;13(11):1850-9.

2.

4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.

Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M.

BMC Bioinformatics. 2006 Nov 13;7:498.

3.

RALEE--RNA ALignment editor in Emacs.

Griffiths-Jones S.

Bioinformatics. 2005 Jan 15;21(2):257-9.

PMID:
15377506
4.
5.

A memory efficient method for structure-based RNA multiple alignment.

DeBlasio D, Bruand J, Zhang S.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):1-11. doi: 10.1109/TCBB.2011.86.

PMID:
21576754
6.

Predicting RNA structure using mutual information.

Freyhult E, Moulton V, Gardner P.

Appl Bioinformatics. 2005;4(1):53-9.

PMID:
16000013
7.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.

Havgaard JH, Lyngsø RB, Gorodkin J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3.

8.

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score.

Hamada M, Sato K, Kiryu H, Mituyama T, Asai K.

Bioinformatics. 2009 Dec 15;25(24):3236-43. doi: 10.1093/bioinformatics/btp580.

PMID:
19808876
9.

RNASAlign: RNA structural alignment system.

Wong TK, Wan KL, Hsu BY, Cheung BW, Hon WK, Lam TW, Yiu SM.

Bioinformatics. 2011 Aug 1;27(15):2151-2. doi: 10.1093/bioinformatics/btr338.

PMID:
21659321
10.

Boulder ALignment Editor (ALE): a web-based RNA alignment tool.

Stombaugh J, Widmann J, McDonald D, Knight R.

Bioinformatics. 2011 Jun 15;27(12):1706-7. doi: 10.1093/bioinformatics/btr258.

11.

RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

Schnattinger T, Schöning U, Marchfelder A, Kestler HA.

Bioinformatics. 2013 Dec 1;29(23):3102-4. doi: 10.1093/bioinformatics/btt536.

PMID:
24045774
12.

Improvement in the accuracy of multiple sequence alignment program MAFFT.

Katoh K, Kuma K, Miyata T, Toh H.

Genome Inform. 2005;16(1):22-33.

PMID:
16362903
13.
14.

The RNA structure alignment ontology.

Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E.

RNA. 2009 Sep;15(9):1623-31. doi: 10.1261/rna.1601409.

15.

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y.

Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612.

PMID:
23060618
16.

The art of editing RNA structural alignments.

Andersen ES.

Methods Mol Biol. 2014;1097:379-94. doi: 10.1007/978-1-62703-709-9_17. Review.

PMID:
24639168
17.

Semi-automated update and cleanup of structural RNA alignment databases.

Gorodkin J, Zwieb C, Knudsen B.

Bioinformatics. 2001 Jul;17(7):642-5.

PMID:
11448882
18.

DNAAlignEditor: DNA alignment editor tool.

Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M, McMullen MD.

BMC Bioinformatics. 2008 Mar 19;9:154. doi: 10.1186/1471-2105-9-154.

19.

RNA structural alignments, part II: non-Sankoff approaches for structural alignments.

Asai K, Hamada M.

Methods Mol Biol. 2014;1097:291-301. doi: 10.1007/978-1-62703-709-9_14.

PMID:
24639165
20.

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