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Items: 1 to 20 of 329

1.

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.

2.

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40.

3.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. doi: 10.1093/nar/gkr245. Epub 2011 May 9.

4.

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.

5.

FFAS03: a server for profile--profile sequence alignments.

Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8.

6.

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.

7.

The HHpred interactive server for protein homology detection and structure prediction.

Söding J, Biegert A, Lupas AN.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8.

8.

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.

Suyama M, Torrents D, Bork P.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12.

9.

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

Moretti S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W600-3.

10.

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

Brandt BW, Heringa J, Leunissen JA.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W255-9. doi: 10.1093/nar/gkn237. Epub 2008 May 7.

11.
12.

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.

13.

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.

Thompson JD, Koehl P, Ripp R, Poch O.

Proteins. 2005 Oct 1;61(1):127-36.

PMID:
16044462
14.

APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C.

Bioinformatics. 2006 Oct 1;22(19):2439-40.

PMID:
17032685
15.

COFFEE: an objective function for multiple sequence alignments.

Notredame C, Holm L, Higgins DG.

Bioinformatics. 1998 Jun;14(5):407-22.

PMID:
9682054
16.

The iRMSD: a local measure of sequence alignment accuracy using structural information.

Armougom F, Moretti S, Keduas V, Notredame C.

Bioinformatics. 2006 Jul 15;22(14):e35-9.

PMID:
16873492
17.

3DCoffee: combining protein sequences and structures within multiple sequence alignments.

O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C.

J Mol Biol. 2004 Jul 2;340(2):385-95.

PMID:
15201059
18.

MyHits: a new interactive resource for protein annotation and domain identification.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W332-5.

19.

The HSSP database of protein structure-sequence alignments and family profiles.

Dodge C, Schneider R, Sander C.

Nucleic Acids Res. 1998 Jan 1;26(1):313-5.

20.

webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Brandt BW, Heringa J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W48-52. doi: 10.1093/nar/gkp279. Epub 2009 May 6.

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