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Items: 1 to 20 of 609

1.

Incremental window-based protein sequence alignment algorithms.

Rangwala H, Karypis G.

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

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.

3.

A comparison of scoring functions for protein sequence profile alignment.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1301-8. Epub 2004 Feb 12.

4.

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

Sauder JM, Arthur JW, Dunbrack RL Jr.

Proteins. 2000 Jul 1;40(1):6-22.

PMID:
10813826
5.

Profile-based string kernels for remote homology detection and motif extraction.

Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C.

J Bioinform Comput Biol. 2005 Jun;3(3):527-50.

PMID:
16108083
6.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

7.

COACH: profile-profile alignment of protein families using hidden Markov models.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1309-18. Epub 2004 Feb 12.

8.
9.

Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms.

Poleksic A, Fienup M.

Bioinformatics. 2008 May 1;24(9):1145-53. doi: 10.1093/bioinformatics/btn097. Epub 2008 Mar 12.

10.

PROMALS: towards accurate multiple sequence alignments of distantly related proteins.

Pei J, Grishin NV.

Bioinformatics. 2007 Apr 1;23(7):802-8. Epub 2007 Jan 31.

11.

Predicting reliable regions in protein alignments from sequence profiles.

Tress ML, Jones D, Valencia A.

J Mol Biol. 2003 Jul 18;330(4):705-18.

PMID:
12850141
12.

SVM-HUSTLE--an iterative semi-supervised machine learning approach for pairwise protein remote homology detection.

Shah AR, Oehmen CS, Webb-Robertson BJ.

Bioinformatics. 2008 Mar 15;24(6):783-90. doi: 10.1093/bioinformatics/btn028. Epub 2008 Feb 1.

13.

A comprehensive system for evaluation of remote sequence similarity detection.

Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV.

BMC Bioinformatics. 2007 Aug 28;8:314.

14.

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.

Kundrotas PJ, Lensink MF, Alexov E.

Int J Biol Macromol. 2008 Aug 15;43(2):198-208. doi: 10.1016/j.ijbiomac.2008.05.004. Epub 2008 May 21.

PMID:
18572239
15.

Protein homology detection using string alignment kernels.

Saigo H, Vert JP, Ueda N, Akutsu T.

Bioinformatics. 2004 Jul 22;20(11):1682-9. Epub 2004 Feb 26.

16.

Learning scoring schemes for sequence alignment from partial examples.

Kim E, Kececioglu J.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):546-56. doi: 10.1109/TCBB.2008.57.

PMID:
18989042
17.

Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments.

Wang C, Yan RX, Wang XF, Si JN, Zhang Z.

Comput Biol Chem. 2011 Oct 12;35(5):308-18. doi: 10.1016/j.compbiolchem.2011.07.006. Epub 2011 Jul 22.

PMID:
22000802
18.

Profile-based string kernels for remote homology detection and motif extraction.

Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C.

Proc IEEE Comput Syst Bioinform Conf. 2004:152-60.

PMID:
16448009
19.

Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT).

Lee MM, Bundschuh R, Chan MK.

Proteins. 2008 May 15;71(3):1409-19.

PMID:
18076050
20.
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