SuiteMSA: Visual tools for multiple sequence alignment comparison and molecular sequence simulation

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Anderson, Catherine L ^a   Strope, Cory L ^b   Moriyama, Etsuko N ^b,c  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b UNIVERSITY OF NEBRASKA   (United States)

^c UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT STATISTICS; BIOLOGICAL RESEARCH; JAVA-BASED APPLICATIONS; MULTIPLE SEQUENCE ALIGNMENTS; RECONSTRUCTION PROGRAMS; VISUAL TOOLS;

BIOLOGY; GRAPHICAL USER INTERFACES; JAVA PROGRAMMING LANGUAGE; RESEARCH; SIMULATORS; TOOLS;

BIOINFORMATICS;

LIPOCALIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; HUMAN; METHODOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; LIPOCALINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 79956190847     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-184     Document Type: Article

References (43)

1. Kemena C, Notredame C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 2009, 25:2455-2465. 10.1093/bioinformatics/btp452, 2752613, 19648142.
2. Gouy M, Guindon S, Gascuel O. SeaView Version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010, 27:221-224. 10.1093/molbev/msp259, 19854763.
3. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948. 10.1093/bioinformatics/btm404, 17846036.
4. Se-Al. , http://tree.bio.ed.ac.uk/software/seal/
5. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25:1189-1191. 10.1093/bioinformatics/btp033, 2672624, 19151095.
6. Löytynoja A, Goldman N. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 2010, 11:579. 10.1186/1471-2105-11-579, 3009689, 21110866.
7. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
8. Shih AC, Lee DT, Lin L, Peng CL, Chen SH, Wu YW, Wong CY, Chou MY, Shiao TC, Hsieh MF. SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. BMC Bioinformatics 2006, 7:103. 10.1186/1471-2105-7-103, 1434773, 16509994.
9. Morrison DA. Why would phylogeneticists ignore computerized sequence alignment?. Syst Biol 2009, 58:150-158. 10.1093/sysbio/syp009, 20525575.
10. Morrison DA. A framework for phylogenetic sequence alignment. Plant Syst Evol 2009, 282:127-149.
11. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
12. Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ. OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics 2003, 4:47. 10.1186/1471-2105-4-47, 280650, 14552658.
13. Stebbings LA, Mizuguchi K. HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res 2004, 32:D203-207. 10.1093/nar/gkh027, 308761, 14681395.
14. Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61:127-136. 10.1002/prot.20527, 16044462.
15. Van Walle I, Lasters I, Wyns L. SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005, 21:1267-1268. 10.1093/bioinformatics/bth493, 15333456.
16. Edgar RC. Quality measures for protein alignment benchmarks. Nucleic Acids Res 2010, 38:2145-2153. 10.1093/nar/gkp1196, 2853116, 20047958.
17. Hillis DM. Approaches for accessing phylogenetic accuracy. Sys Biol 1995, 44:3-16.
18. Fletcher W, Yang Z. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol 2009, 26:1879-1888. 10.1093/molbev/msp098, 2712615, 19423664.
19. Stoye J, Evers D, Meyer F. Rose: generating sequence families. Bioinformatics 1998, 14:157-163. 10.1093/bioinformatics/14.2.157, 9545448.
20. Cartwright RA. DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 2005, 21:iii31-iii38. 10.1093/bioinformatics/bti1200, 16306390.
21. Rosenberg MS. MySSP: non-stationary evolutionary sequence simulation, including indels. Evol Bioinform Online 2005, 1:81-83. 2658873, 19325855.
22. Pang A, Smith AD, Nuin PA, Tillier ER. SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics 2005, 6:236. 10.1186/1471-2105-6-236, 1261159, 16188037.
23. Hall BG. Simulating DNA coding sequence evolution with EvolveAGene 3. Mol Biol Evol 2008, 25:688-695. 10.1093/molbev/msn008, 18192698.
24. Strope CL, Abel K, Scott SD, Moriyama EN. Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol 2009, 26:2581-2593. 10.1093/molbev/msp174, 2760465, 19651852.
25. Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B. DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics 2005, 6:66. 10.1186/1471-2105-6-66, 1087830, 15784139.
26. Flower DR, North ACT, Attwood TK. Structure and sequence relationships in the lipocalins and related proteins. Protein Sci 1993, 2:753-761. 10.1002/pro.5560020507, 2142497, 7684291.
27. Sánchez D, Ganfornina MD, Gutiérrez G, Marín A. Exon-intron structure and evolution of the lipocalin gene family. Mol Biol Evol 2003, 20:775-783. 10.1093/molbev/msg079, 12679526.
28. Strope CL, Scott SD, Moriyama EN. indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. Mol Biol Evol 2007, 24:640-649.
29. Jones T. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292:195-202. 10.1006/jmbi.1999.3091, 10493868.
30. Thompson J, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 1999, 27:2682-2690. 10.1093/nar/27.13.2682, 148477, 10373585.
31. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9:286-298. 10.1093/bib/bbn013, 18372315.
32. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113. 10.1186/1471-2105-5-113, 517706, 15318951.
33. Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 2010, 38:D161-D166. 10.1093/nar/gkp885, PMC2808866, 19858104.
34. PROSITE: Database of protein domains, families and functional sites. , http://ca.expasy.org/prosite/
35. Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21:2104-2105. 10.1093/bioinformatics/bti263, 15647292.
36. PROTTEST: Selection of best-fit models of protein evolution. , http://darwin.uvigo.es/software/prottest.html
37. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704. 10.1080/10635150390235520, 14530136.
38. Drummond A, Strimmer K. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 2001, 17:662-663. 10.1093/bioinformatics/17.7.662, 11448888.
39. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18:691-699.
40. Clustal programs download site. , http://www.clustal.org/download/current/
41. MUSCLE program download site. , http://www.drive5.com/muscle/
42. Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008, 320:1632-1635. 10.1126/science.1158395, 18566285.
43. Schneider T, Stephens R. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18:6097-6100. 10.1093/nar/18.20.6097, 332411, 2172928.