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Results: 1 to 20 of 69

1.

Scoring pairwise genomic sequence alignments.

Chiaromonte F, Yap VB, Miller W.

Pac Symp Biocomput. 2002:115-26.

PMID:
11928468
[PubMed - indexed for MEDLINE]
2.

PipMaker: a World Wide Web server for genomic sequence alignments.

Elnitski L, Riemer C, Schwartz S, Hardison R, Miller W.

Curr Protoc Bioinformatics. 2003 Feb;Chapter 10:Unit 10.2. doi: 10.1002/0471250953.bi1002s00.

PMID:
18428692
[PubMed - indexed for MEDLINE]
3.

Benchmarking tools for the alignment of functional noncoding DNA.

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.

BMC Bioinformatics. 2004 Jan 21;5:6.

PMID:
14736341
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Distinguishing regulatory DNA from neutral sites.

Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F.

Genome Res. 2003 Jan;13(1):64-72.

PMID:
12529307
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Multiple sequence alignments of partially coding nucleic acid sequences.

Stocsits RR, Hofacker IL, Fried C, Stadler PF.

BMC Bioinformatics. 2005 Jun 28;6:160.

PMID:
15985156
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.

Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R.

Genomics. 2002 Dec;80(6):681-90.

PMID:
12504859
[PubMed - indexed for MEDLINE]
7.
8.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

Kiryu H, Kin T, Asai K.

Bioinformatics. 2007 Feb 15;23(4):434-41. Epub 2006 Dec 20.

PMID:
17182698
[PubMed - indexed for MEDLINE]
Free Article
9.

A novel heuristic for local multiple alignment of interspersed DNA repeats.

Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):180-9. doi: 10.1109/TCBB.2009.9.

PMID:
19407343
[PubMed - indexed for MEDLINE]
10.

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.

PMID:
16542424
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

On the significance of sequence alignments when using multiple scoring matrices.

Frommlet F, Futschik A, Bogdan M.

Bioinformatics. 2004 Apr 12;20(6):881-7. Epub 2004 Jan 29.

PMID:
14751984
[PubMed - indexed for MEDLINE]
Free Article
12.

Genomic multiple sequence alignments: refinement using a genetic algorithm.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2005 Aug 8;6:200.

PMID:
16086841
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Considerations in the identification of functional RNA structural elements in genomic alignments.

Babak T, Blencowe BJ, Hughes TR.

BMC Bioinformatics. 2007 Jan 30;8:33.

PMID:
17263882
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

RNA secondary structural alignment with conditional random fields.

Sato K, Sakakibara Y.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii237-42.

PMID:
16204111
[PubMed - indexed for MEDLINE]
Free Article
15.

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Elnitski L, Riemer C, Burhans R, Hardison R, Miller W.

Curr Protoc Bioinformatics. 2005 Apr;Chapter 10:Unit10.4. doi: 10.1002/0471250953.bi1004s9.

PMID:
18428743
[PubMed - indexed for MEDLINE]
16.

Towards realistic benchmarks for multiple alignments of non-coding sequences.

Kim J, Sinha S.

BMC Bioinformatics. 2010 Jan 26;11:54. doi: 10.1186/1471-2105-11-54.

PMID:
20102627
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A simulated annealing algorithm for finding consensus sequences.

Keith JM, Adams P, Bryant D, Kroese DP, Mitchelson KR, Cochran DA, Lala GH.

Bioinformatics. 2002 Nov;18(11):1494-9.

PMID:
12424121
[PubMed - indexed for MEDLINE]
Free Article
18.

How should gaps be treated in parsimony? A comparison of approaches using simulation.

Ogden TH, Rosenberg MS.

Mol Phylogenet Evol. 2007 Mar;42(3):817-26. Epub 2006 Aug 22. Erratum in: Mol Phylogenet Evol. 2008 Feb;46(2):807-8.

PMID:
17011794
[PubMed - indexed for MEDLINE]
19.

Identification and measurement of neighbor-dependent nucleotide substitution processes.

Arndt PF, Hwa T.

Bioinformatics. 2005 May 15;21(10):2322-8. Epub 2005 Mar 15.

PMID:
15769841
[PubMed - indexed for MEDLINE]
Free Article
20.

Comparative annotation of viral genomes with non-conserved gene structure.

de Groot S, Mailund T, Hein J.

Bioinformatics. 2007 May 1;23(9):1080-9. Epub 2007 Mar 6.

PMID:
17341494
[PubMed - indexed for MEDLINE]
Free Article

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