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Results: 1 to 20 of 278

1.

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.

Pirovano W, Feenstra KA, Heringa J.

Bioinformatics. 2008 Feb 15;24(4):492-7. doi: 10.1093/bioinformatics/btm636. Epub 2008 Jan 2.

PMID:
18174178
[PubMed - indexed for MEDLINE]
Free Article
2.

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

PMID:
17488755
[PubMed - indexed for MEDLINE]
Free Article
3.

From analysis of protein structural alignments toward a novel approach to align protein sequences.

Sunyaev SR, Bogopolsky GA, Oleynikova NV, Vlasov PK, Finkelstein AV, Roytberg MA.

Proteins. 2004 Feb 15;54(3):569-82.

PMID:
14748004
[PubMed - indexed for MEDLINE]
4.

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.

Pandit SB, Skolnick J.

BMC Bioinformatics. 2008 Dec 12;9:531. doi: 10.1186/1471-2105-9-531.

PMID:
19077267
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The meaning of alignment: lessons from structural diversity.

Pirovano W, Feenstra KA, Heringa J.

BMC Bioinformatics. 2008 Dec 23;9:556. doi: 10.1186/1471-2105-9-556.

PMID:
19105835
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Multiple alignment by sequence annealing.

Schwartz AS, Pachter L.

Bioinformatics. 2007 Jan 15;23(2):e24-9.

PMID:
17237099
[PubMed - indexed for MEDLINE]
Free Article
7.

Local weighting schemes for protein multiple sequence alignment.

Heringa J.

Comput Chem. 2002 Jul;26(5):459-77.

PMID:
12144176
[PubMed - indexed for MEDLINE]
8.

COFFEE: an objective function for multiple sequence alignments.

Notredame C, Holm L, Higgins DG.

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

PMID:
9682054
[PubMed - indexed for MEDLINE]
Free Article
9.

Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods.

Natt NK, Kaur H, Raghava GP.

Proteins. 2004 Jul 1;56(1):11-8.

PMID:
15162482
[PubMed - indexed for MEDLINE]
10.

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.

Fariselli P, Finelli M, Marchignoli D, Martelli PL, Rossi I, Casadio R.

Bioinformatics. 2003 Mar 1;19(4):500-5.

PMID:
12611805
[PubMed - indexed for MEDLINE]
Free Article
11.

Iterative refinement of structure-based sequence alignments by Seed Extension.

Kim C, Tai CH, Lee B.

BMC Bioinformatics. 2009 Jul 9;10:210. doi: 10.1186/1471-2105-10-210.

PMID:
19589133
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A genetic algorithm for multiple molecular sequence alignment.

Zhang C, Wong AK.

Comput Appl Biosci. 1997 Dec;13(6):565-81.

PMID:
9475984
[PubMed - indexed for MEDLINE]
13.

The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.

Simossis VA, Heringa J.

Comput Biol Chem. 2004 Dec;28(5-6):351-66.

PMID:
15556476
[PubMed - indexed for MEDLINE]
14.

Remote homology detection of integral membrane proteins using conserved sequence features.

Bernsel A, Viklund H, Elofsson A.

Proteins. 2008 May 15;71(3):1387-99.

PMID:
18076048
[PubMed - indexed for MEDLINE]
15.

A local multiple alignment method for detection of non-coding RNA sequences.

Tabei Y, Asai K.

Bioinformatics. 2009 Jun 15;25(12):1498-505. doi: 10.1093/bioinformatics/btp261. Epub 2009 Apr 17.

PMID:
19376823
[PubMed - indexed for MEDLINE]
Free Article
16.

Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method.

Cserzö M, Wallin E, Simon I, von Heijne G, Elofsson A.

Protein Eng. 1997 Jun;10(6):673-6.

PMID:
9278280
[PubMed - indexed for MEDLINE]
Free Article
17.

A simple genetic algorithm for multiple sequence alignment.

Gondro C, Kinghorn BP.

Genet Mol Res. 2007 Oct 5;6(4):964-82.

PMID:
18058716
[PubMed - indexed for MEDLINE]
Free Article
18.

Incremental window-based protein sequence alignment algorithms.

Rangwala H, Karypis G.

Bioinformatics. 2007 Jan 15;23(2):e17-23.

PMID:
17237087
[PubMed - indexed for MEDLINE]
Free Article
19.

Multiple sequence alignment.

Edgar RC, Batzoglou S.

Curr Opin Struct Biol. 2006 Jun;16(3):368-73. Epub 2006 May 5. Review.

PMID:
16679011
[PubMed - indexed for MEDLINE]
20.

Combining many multiple alignments in one improved alignment.

Bucka-Lassen K, Caprani O, Hein J.

Bioinformatics. 1999 Feb;15(2):122-30.

PMID:
10089197
[PubMed - indexed for MEDLINE]
Free Article

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