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Items: 1 to 20 of 78

1.

Multiple genome comparison based on overlap regions of pairwise local alignments.

Jahn K, Sudek H, Stoye J.

BMC Bioinformatics. 2012;13 Suppl 19:S7. doi: 10.1186/1471-2105-13-S19-S7. Epub 2012 Dec 19.

2.

Structure alignment based on coding of local geometric measures.

Chang PL, Rinne AW, Dewey TG.

BMC Bioinformatics. 2006 Jul 14;7:346.

3.

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
4.

Multiple whole-genome alignments without a reference organism.

Dubchak I, Poliakov A, Kislyuk A, Brudno M.

Genome Res. 2009 Apr;19(4):682-9. doi: 10.1101/gr.081778.108. Epub 2009 Jan 28.

5.

Using multiple alignments to improve seeded local alignment algorithms.

Flannick J, Batzoglou S.

Nucleic Acids Res. 2005 Aug 12;33(14):4563-77. Print 2005.

6.

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.

PMID:
16269416
7.

Automatic assessment of alignment quality.

Lassmann T, Sonnhammer EL.

Nucleic Acids Res. 2005 Dec 16;33(22):7120-8. Print 2005.

8.
9.

Fast and sensitive multiple alignment of large genomic sequences.

Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B.

BMC Bioinformatics. 2003 Dec 23;4:66.

10.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

11.

Stochastic pairwise alignments.

Mückstein U, Hofacker IL, Stadler PF.

Bioinformatics. 2002;18 Suppl 2:S153-60.

PMID:
12385998
12.

ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts.

Choi K, Kim S.

BMC Bioinformatics. 2008 Mar 6;9:145. doi: 10.1186/1471-2105-9-145.

13.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

14.

Evolutionary HMMs: a Bayesian approach to multiple alignment.

Holmes I, Bruno WJ.

Bioinformatics. 2001 Sep;17(9):803-20.

PMID:
11590097
15.

Glocal alignment: finding rearrangements during alignment.

Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S.

Bioinformatics. 2003;19 Suppl 1:i54-62.

PMID:
12855437
16.

Clustering of main orthologs for multiple genomes.

Fu Z, Jiang T.

J Bioinform Comput Biol. 2008 Jun;6(3):573-84.

PMID:
18574863
17.

PhyLAT: a phylogenetic local alignment tool.

Sun H, Buhler JD.

Bioinformatics. 2012 May 15;28(10):1336-44. doi: 10.1093/bioinformatics/bts158. Epub 2012 Apr 6.

18.

Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes.

Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y.

PLoS One. 2010 Sep 24;5(9):e12651. doi: 10.1371/journal.pone.0012651.

19.

Annotation confidence score for genome annotation: a genome comparison approach.

Yang Y, Gilbert D, Kim S.

Bioinformatics. 2010 Jan 1;26(1):22-9. doi: 10.1093/bioinformatics/btp613. Epub 2009 Oct 24.

PMID:
19855104
20.

Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.

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