DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

Cannon SB, Kozik A, Chan B, Michelmore R, Young ND.

Genome Biol. 2003;4(10):R68. Epub 2003 Sep 19.

PMID: 14519203 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

How to usefully compare homologous plant genes and chromosomes as DNA sequences.

Lyons E, Freeling M.

Plant J. 2008 Feb;53(4):661-73. Review.

PMID: 18269575 [PubMed - indexed for MEDLINE]

Related Articles

Gene structure prediction in syntenic DNA segments.

Moore JE, Lake JA.

Nucleic Acids Res. 2003 Dec 15;31(24):7271-9.

PMID: 14654703 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Comparative map and trait viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments.

Sawkins MC, Farmer AD, Hoisington D, Sullivan J, Tolopko A, Jiang Z, Ribaut JM.

Plant Mol Biol. 2004 Oct;56(3):465-80.

PMID: 15604756 [PubMed - indexed for MEDLINE]

Related Articles

Visualization of comparative genomic analyses by BLAST score ratio.

Rasko DA, Myers GS, Ravel J.

BMC Bioinformatics. 2005 Jan 5;6:2.

PMID: 15634352 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.

Sinha AU, Meller J.

BMC Bioinformatics. 2007 Mar 8;8:82.

PMID: 17343765 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.

Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J.

BMC Bioinformatics. 2006 Oct 12;7:447.

PMID: 17038171 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

GeneViTo: visualizing gene-product functional and structural features in genomic datasets.

Vernikos GS, Gkogkas CG, Promponas VJ, Hamodrakas SJ.

BMC Bioinformatics. 2003 Oct 31;4:53.

PMID: 14594459 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

PILER: identification and classification of genomic repeats.

Edgar RC, Myers EW.

Bioinformatics. 2005 Jun;21 Suppl 1:i152-8.

PMID: 15961452 [PubMed - indexed for MEDLINE]

Related Articles

Genome rearrangements in mammalian evolution: lessons from human and mouse genomes.

Pevzner P, Tesler G.

Genome Res. 2003 Jan;13(1):37-45.

PMID: 12529304 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

MaGe: a microbial genome annotation system supported by synteny results.

Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Médigue C.

Nucleic Acids Res. 2006 Jan 10;34(1):53-65. Print 2006.

PMID: 16407324 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Segmental duplication density decrease with distance to human-mouse breaks of synteny.

Sainz J, Rovensky P, Gudjonsson SA, Thorleifsson G, Stefansson K, Gulcher JR.

Eur J Hum Genet. 2006 Feb;14(2):216-21.

PMID: 16306878 [PubMed - indexed for MEDLINE]

Related Articles

Computational gene finding in plants.

Pertea M, Salzberg SL.

Plant Mol Biol. 2002 Jan;48(1-2):39-48. Review.

PMID: 11860211 [PubMed - indexed for MEDLINE]

Related Articles

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser.

Byrne KP, Wolfe KH.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D452-5.

PMID: 16381909 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Brown CT, Xie Y, Davidson EH, Cameron RA.

BMC Bioinformatics. 2005 Mar 24;6:70.

PMID: 15790396 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T.

J Comput Biol. 2007 Nov;14(9):1160-75.

PMID: 17990975 [PubMed - indexed for MEDLINE]

Related Articles

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.

PMID: 15590941 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.

Hampson S, McLysaght A, Gaut B, Baldi P.

Genome Res. 2003 May;13(5):999-1010. Epub 2003 Apr 14.

PMID: 12695327 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes.

Jung S, Main D, Staton M, Cho I, Zhebentyayeva T, Arús P, Abbott A.

BMC Genomics. 2006 Apr 14;7:81.

PMID: 16615871 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC

Sockeye: a 3D environment for comparative genomics.

Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ.

Genome Res. 2004 May;14(5):956-62.

PMID: 15123592 [PubMed - indexed for MEDLINE]

Related Articles Free article in PMC