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Results: 1 to 20 of 99

Similar articles for PubMed (Select 17387111)

1.

Ngila: global pairwise alignments with logarithmic and affine gap costs.

Cartwright RA.

Bioinformatics. 2007 Jun 1;23(11):1427-8. Epub 2007 Mar 25.

2.

Logarithmic gap costs decrease alignment accuracy.

Cartwright RA.

BMC Bioinformatics. 2006 Dec 5;7:527.

3.

DNA assembly with gaps (Dawg): simulating sequence evolution.

Cartwright RA.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8.

4.

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

Kim J, Sinha S.

Bioinformatics. 2007 Feb 1;23(3):289-97. Epub 2006 Nov 15.

5.

PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.

Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA.

BMC Bioinformatics. 2011 Jan 7;12:10. doi: 10.1186/1471-2105-12-10.

6.

ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.

Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T.

BMC Bioinformatics. 2008 Feb 22;9:112. doi: 10.1186/1471-2105-9-112.

7.
8.

The tree alignment problem.

Varón A, Wheeler WC.

BMC Bioinformatics. 2012 Nov 9;13:293. doi: 10.1186/1471-2105-13-293.

9.

MAP2: multiple alignment of syntenic genomic sequences.

Ye L, Huang X.

Nucleic Acids Res. 2005 Jan 7;33(1):162-70. Print 2005.

10.

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
11.

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.

12.

Local sequence alignments with monotonic gap penalties.

Mott R.

Bioinformatics. 1999 Jun;15(6):455-62.

13.
14.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

15.

Discovering and detecting transposable elements in genome sequences.

Bergman CM, Quesneville H.

Brief Bioinform. 2007 Nov;8(6):382-92. Epub 2007 Oct 10. Review.

16.

COMPAM :visualization of combining pairwise alignments for multiple genomes.

Lee D, Choi JH, Dalkilic MM, Kim S.

Bioinformatics. 2006 Jan 15;22(2):242-4. Epub 2005 Nov 3.

17.

DIALIGN: finding local similarities by multiple sequence alignment.

Morgenstern B, Frech K, Dress A, Werner T.

Bioinformatics. 1998;14(3):290-4.

18.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
19.

SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.

Ho JW, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS.

Bioinformatics. 2006 Sep 1;22(17):2162-3. Epub 2006 Jun 9.

20.

Using evolutionary Expectation Maximization to estimate indel rates.

Holmes I.

Bioinformatics. 2005 May 15;21(10):2294-300. Epub 2005 Feb 24.

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