Description of my initial results to identify NeSL-1 full length and truncated elements. Previously only identified in C elegans, multiple copies were identified in C brenneri, C japonica, and C remanei. A single truncated copy was seen ijn C briggsae. Completed in 2010.

1. 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

15. 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.

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. Epub
2008 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.

32. C elegans/C remanei

33. C japonica/C brenneri

37. C elegans

38. C brenneri

39. C remanei

40. C japonica

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

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

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

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

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

74. 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.