SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools

BMC Bioinformatics
Arthur Chun-Chieh ShihMu-Fen Hsieh

Abstract

Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence analysis, a biologist is usually faced with the questions of how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question of whether poorly aligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. Although several systematic evaluations of multiple sequence alignment (MSA) programs have been proposed, they may not provide a standard-bearer for most biologists because those poorly aligned regions in these evaluations are never discussed. Thus, a tool that allows cross comparison of the alignment results obtained by different tools simultaneously could help a biologist evaluate their correctness and accuracy. In this paper, we present a versatile alignment visualization system, called SinicView, (for Sequence-aligning INnovative and Interactive Comparison VIEWer), which allows the user to efficiently compare and evaluate assorted nucleotide alignment results...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
May 15, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Dec 3, 1999·The International Journal of Biochemistry & Cell Biology·L M BartonA R Green
Apr 26, 2000·Genome Research·S SchwartzW Miller
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Mar 27, 2001·Current Biology : CB·E V Koonin
May 4, 2002·Nature Reviews. Genetics·Mark A Batzer, Prescott L Deininger
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jul 27, 2002·Science·Samuel AparicioSydney Brenner
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Jan 1, 2003·Nature·Roland HeiligJean Weissenbach
Jan 17, 2003·Genome Research·Kelly A FrazerRoss C Hardison
Jan 17, 2003·Genome Research·Olivier CouronneInna Dubchak
Jan 17, 2003·Genome Research·Nick BrayLior Pachter
Mar 26, 2003·Genome Research·Michael BrudnoSerafim Batzoglou
Apr 3, 2003·Nature Reviews. Genetics·Abel Ureta-VidalEwan Birney
Jun 5, 2003·Molecular Biology and Evolution·Arthur Chun-Chieh Shih, Wen-Hsiung Li
Jun 26, 2003·Nucleic Acids Research·Scott SchwartzWebb Miller
Oct 4, 2003·Science·Emmanouil T DermitzakisStylianos E Antonarakis
Oct 14, 2003·BMC Bioinformatics·G P S RaghavaGeoffrey J Barton
Dec 9, 2003·Genome Biology·Inna Dubchak, Kelly Frazer
Jan 23, 2004·BMC Bioinformatics·Daniel A PollardMichael B Eisen
Mar 23, 2004·Bioinformatics·Nameeta ShahInna Dubchak
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 2, 2004·Nature·Richard A GibbsUNKNOWN Rat Genome Sequencing Project Consortium
Apr 3, 2004·Genome Research·Michael BrudnoInna Dubchak
Apr 3, 2004·Genome Research·Nicolas Bray, Lior Pachter
Apr 3, 2004·Genome Research·Mathieu BlanchetteWebb Miller
Jun 10, 2004·BMC Bioinformatics·D A PollardM B Eisen
Jun 25, 2004·Nucleic Acids Research·Gabriela G Loots, Ivan Ovcharenko
Jun 25, 2004·Nucleic Acids Research·Kelly A FrazerInna Dubchak
Oct 16, 2004·Annual Review of Genomics and Human Genetics·Webb MillerRoss C Hardison
Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium
Dec 14, 2004·Nature·UNKNOWN International Chicken Genome Sequencing Consortium
Dec 21, 2004·Nucleic Acids Research·T HubbardE Birney
Apr 5, 2005·Pediatric Pulmonology·Victoria A McCarthy, Ann Harris

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Citations

Jun 12, 2009·Omics : a Journal of Integrative Biology·Hsueh-Wei ChangCheng-Hong Yang
Jul 25, 2009·BMC Bioinformatics·Francisco FernandesAna T Freitas
May 24, 2011·BMC Bioinformatics·Catherine L AndersonEtsuko N Moriyama
Apr 11, 2015·Evolutionary Bioinformatics Online·Muhammad Tariq PervezMaryam Javed
Jan 18, 2018·BMC Genomics·Christine JandrasitsBernhard Y Renard
May 11, 2007·Annual Review of Genomics and Human Genetics·Mathieu Blanchette
Sep 20, 2006·International Journal of Biological Macromolecules·Linden E HigginsJesus Vargas

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Software Mentioned

rVISTA
Window XP
Fedora Core
COFFEE
BlastZ
SinicView ( Sequence - aligning INnovative and Interactive Com...
ATVtree
GS
RepeatMasker
MAVID

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