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Items: 1 to 20 of 68

1.

Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment.

Kjer KM, Gillespie JJ, Ober KA.

Syst Biol. 2007 Feb;56(1):133-46. No abstract available.

PMID:
17366144
3.

Phylogeny estimation and alignment via POY versus Clustal + PAUP*: a response to Ogden and Rosenberg (2007).

Lehtonen S.

Syst Biol. 2008 Aug;57(4):653-7. doi: 10.1080/10635150802302476. No abstract available.

PMID:
18709601
4.

The order of sequence alignment can bias the selection of tree topology.

Lake JA.

Mol Biol Evol. 1991 May;8(3):378-85. No abstract available.

PMID:
2072863
5.

The RNA structure alignment ontology.

Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E.

RNA. 2009 Sep;15(9):1623-31. doi: 10.1261/rna.1601409. Epub 2009 Jul 21.

6.

Search-based optimization.

Wheeler WC.

Cladistics. 2003 Aug;19(4):348-55.

PMID:
14531408
8.

Protein multiple sequence alignment.

Do CB, Katoh K.

Methods Mol Biol. 2008;484:379-413. doi: 10.1007/978-1-59745-398-1_25. Review.

PMID:
18592193
9.

PC/GENE: sequence comparisons and homologies.

Bender PK, Larson TJ.

Methods Mol Biol. 1994;24:283-8. No abstract available.

PMID:
8205199
10.

How well does the HoT score reflect sequence alignment accuracy?

Hall BG.

Mol Biol Evol. 2008 Aug;25(8):1576-80. doi: 10.1093/molbev/msn103. Epub 2008 May 4.

PMID:
18458029
11.

Lagomorphs misplaced by more characters and fewer taxa.

Halanych KM.

Syst Biol. 1998 Mar;47(1):138-46. No abstract available.

PMID:
12064234
12.

PROMALS3D web server for accurate multiple protein sequence and structure alignments.

Pei J, Tang M, Grishin NV.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W30-4. doi: 10.1093/nar/gkn322. Epub 2008 May 24.

13.

UniPrime: a workflow-based platform for improved universal primer design.

Bekaert M, Teeling EC.

Nucleic Acids Res. 2008 Jun;36(10):e56. doi: 10.1093/nar/gkn191. Epub 2008 Apr 19.

14.

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.

15.

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities.

Roshan U, Chikkagoudar S, Livesay DR.

BMC Bioinformatics. 2008 Jan 28;9:61. doi: 10.1186/1471-2105-9-61.

16.

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.

17.

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Satija R, Pachter L, Hein J.

Bioinformatics. 2008 May 15;24(10):1236-42. doi: 10.1093/bioinformatics/btn104. Epub 2008 Mar 18.

PMID:
18353788
18.

Exploring an alignment free approach for protein classification and structural class prediction.

Deschavanne P, Tufféry P.

Biochimie. 2008 Apr;90(4):615-25. Epub 2007 Nov 19.

PMID:
18067866
19.

Sequence analyses and a unifying system of virus taxonomy: consensus via consent.

Calisher CH, Horzinek MC, Mayo MA, Ackermann HW, Maniloff J.

Arch Virol. 1995;140(11):2093-9. No abstract available.

PMID:
7503705
20.

Murlet: a practical multiple alignment tool for structural RNA sequences.

Kiryu H, Tabei Y, Kin T, Asai K.

Bioinformatics. 2007 Jul 1;23(13):1588-98. Epub 2007 Apr 25.

PMID:
17459961

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