Identification of NeSL-1 in Caenorhabitis

N M-Coffee: combining multiple sequence alignment methods with T-Coffee.

Wallace IM, O'Sullivan O, Higgins DG, Notredame C.

Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.Poirot O, O'Toole E, Notredame C.Nucleic Acids Res. 2003 Jul 1;31(13):3503-6.T-Coffee: A novel method for fast and accurate multiple sequence alignment.Notredame C, Higgins DG, Heringa J.J Mol Biol. 2000 Sep 8;302(1):205-17.

R-Coffee: a web server for accurately aligning noncoding RNA sequences.Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C.Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W10-3. Epub2008 May 15.

R-Coffee: a method for multiple alignment of non-coding RNA.Wilm A, Higgins DG, Notredame C.Nucleic Acids Res. 2008 May;36(9):e52. Epub 2008 Apr 17.

C elegans/C remanei

C japonica/C brenneri

C elegans

C brenneri

C remanei

C japonica

C elegans;1-115 | C brenneri 1-115C remanei; 1-115 | C japonica 1-115

C elegans;1-115 | C brenneri 1-115C remanei; 1-115 | C japonica 1-115

C elegans;1-115 | C brenneri 1-115C remanei; 1-115 | C japonica 1-115

C elegans;1-115 | C brenneri 1-115C remanei; 1-115 | C japonica 1-115

C elegans;1-115 | C brenneri 1-115C remanei; 1-115 | C japonica 1-115

1. Cross-Genome Screening of Novel Sequence-Specific Non-LTR Retrotransposons: Various Multicopy RNA Genes and Microsatellites Are Selected as Targets; Kenji K. Kojima and Haruhiko Fujiwara; Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo1

2. S. Janssen and R. Giegerich. Faster computation of exact RNA shape probabilities. Bioinformatics, 26(5), 2010.

3. P. Steffen, B. Voß, M. Rehmsmeier, J. Reeder, and R. Giegerich. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4), 2006.

4. J. Reeder and R. Giegerich. Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics, 21(17), 2005.

5. R. Giegerich, B. Voß and M. Rehmsmeier. Abstract Shapes of RNA, Nucl. Ac. Res., 32(16), 2004.

6. B. Voß, R.Giegerich and M. Rehmsmeier. Complete probabilistic analysis of RNA shapes, BMC Biology, 4:5, 2006.