AlignMiner: A Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

Algorithms for Molecular Biology

Volumn 5, Issue 1, 2010, Pages

  Guerrero, Darío ^a   Bautista, Rocío ^a   Villalobos, David P ^a   Cantón, Francisco R ^a   Claros, M Gonzalo ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77952832380     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-5-24     Document Type: Article

References (40)

1. Capra JA, Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics 2007, 23(15):1875-1882. 10.1093/bioinformatics/btm270, 17519246.
2. Kim KM, Sung S, Caetano-Anollés G, Han JY, Kim H. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res 2008, 36(17):e110. 10.1093/nar/gkn485, 2553584, 18676448.
3. Merkl R, Zwick M. H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. BMC Bioinformatics 2008, 9:151. 10.1186/1471-2105-9-151, 2323388, 18366663.
4. Kemena K, Notredame C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 2009, 25(19):2455-2465. 10.1093/bioinformatics/btp452, 2752613, 19648142.
5. Czechowski T, Bari RP, Stitt M, Scheible W, Udvardi MK. Real-time RT-PCR profiling of over 1400 Arabidospis transcription factors: unprecedented sensity reveals novel root- and shoot-specific genes. Plant J 2004, 38:366-379. 10.1111/j.1365-313X.2004.02051.x, 15078338.
6. Claros MG, Crespillo R, Aguilar ML, Cánovas FM. DNA Fingerprinting and classification of geographically related genotypes of olive-tree (Olea europaea L.). Euphytica 2000, 116:131-142.
7. Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker G, Spangenberg GC, Edwards D. SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 2005, (33 Web Server):W493-5. 10.1093/nar/gki462, 1160223, 15980519.
8. Ferri G, Alù M, Corradini B, Licata M, Beduschi G. Species Identification Through DNA Barcodes. Genet Test Mol Biomarkers 2009, 13:421-426. 10.1089/gtmb.2008.0144, 19405876.
9. Bautista R, Crespillo R, Canovas FM, Claros MG. Identification of olive-tree cultivars with SCAR markers. Euphytica 2003, 129:33-41.
10. Geysen HM, Rodda SJ, Mason TJ. The delineation of peptides able to mimic assembled epitopes. Ciba Found Symp 1986, 119:130-149.
11. Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu PP, Gibbs RA, Buetow KH. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol 2005, 1(5):e53. 10.1371/journal.pcbi.0010053, 1274293, 16261194.
12. D RP, Del-Favero J. novoSNP3: variant detection and sequence annotation in resequencing projects. Methods Mol Biol 2007, 396:331-344.
13. Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP. SNP-PHAGE-High throughput SNP discovery pipeline. BMC Bioinformatics 2006, 7:468. 10.1186/1471-2105-7-468, 1626092, 17059604.
14. Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics 2009, 25(18):2434-2435. 10.1093/bioinformatics/btp403, 2735664, 19574284.
15. Chang HW, Chuang LY, Cheng YH, Hung YC, Wen CH, Gu DL, Yang CH. Prim-SNPing: a primer designer for cost-effective SNP genotyping. Biotechniques 2009, 46(6):421-431. 10.2144/000113092, 19480636.
16. Tang J, Leunissen JA, Voorrips RE, van der Linden CG, Vosman B. HaploSNPer: a web-based allele and SNP detection tool. BMC Genetics 2008, 9:23. 10.1186/1471-2156-9-23, 2288614, 18307806.
17. Panitz F, Stengaard H, Hornshoj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Hoj A, Vingborg RK, Zahn B, Wang X, Wernersson R, Jorgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics 2007, 23(13):i387-i391. 10.1093/bioinformatics/btm192, 17646321.
18. Wegrzyn JL, Lee JM, Liechty J, Neale DB. PineSAP - sequence alignment and SNP identification pipeline. Bioinformatics 2009, 25(19):2609-2610. 10.1093/bioinformatics/btp477, 2752621, 19667082.
19. Kim N, Lee G. QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. Bioinformatics 2007, 23(17):2331-2333. 10.1093/bioinformatics/btm343, 17599926.
20. Gadberry MD, Malcomber ST, Doust AN, Kellogg EA. Primaclade--a flexible tool to find conserved PCR primers across multiple species. Bioinformatics 2005, 21(7):1263-1264. 10.1093/bioinformatics/bti134, 15539448.
21. Rascol VL, Levasseur A, Chabrol O, Grusea S, Gouret P, Danchin EGJ, Pontarotti P. CASSIOPE: An expert system for conserved regions searches. BMC Bioinformatics 2009, (10):284. 10.1186/1471-2105-10-284, 2756280, 19740451.
22. Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C, Fuellen G, Gilbert J, Korf I, Lapp H, Lehvasläiho H, Matsalla C, Mungall C, Osborne B, Pocock M, Schattner P, Senger M, Stein L, Stupka E, Wilkinson M, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611-8. 10.1101/gr.361602, 187536, 12368254.
23. Garret J. Ajax: A New Approach to Web Applications. Adaptive Path 2005,
24. Java Script Object Notation. 1999, , http://www.json.org
25. Wallace IM, O'Sullivan O, Higgins DG, Notredame C. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res 2006, 34(6):1692-1699. 10.1093/nar/gkl091, 1410914, 16556910.
26. Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C. The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res 2007, 35:W645-8. 10.1093/nar/gkm333, 1933118, 17526519., http://www.tcoffee.org
27. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 1988, 16(22):10881-90. 10.1093/nar/16.22.10881, 338945, 2849754.
28. Lassmann T, Frings O, Sonnhammer ELL. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res 2009, 37(3):858-65. 10.1093/nar/gkn1006, 2647288, 19103665.
29. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85:2444-48. 10.1073/pnas.85.8.2444, 280013, 3162770.
30. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
31. Sean R. Where did the BLOSUM62 alignment score matrix come from?. Nature Biotechnology 2004, 22:1035-1036. 10.1038/nbt0804-1035, 15286655.
32. Blosum62 matrix. , http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62
33. Pinto FL, Svensson H, Lindblad P. Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes. BMC Biotecnology 2007, 7:73., http://www.biomedcentral.com/1472-6750/7/73/
34. PCR amplification at BioPHP. 2009, , http://biophp.org/minitools/pcr_amplification/demo.php
35. Bikandi J, San Millán R, Rementeria A, Garaizar J. In silico analysis of complete bacterial genomes: PCR, AFLP-PCR, and endonuclease restriction. Bioinformatics 2004, 20(5):798-799. 10.1093/bioinformatics/btg491, 14752001.
36. Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18(20):6097-6100. 10.1093/nar/18.20.6097, 332411, 2172928.
37. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034-50. 10.1101/gr.3715005, 1182216, 16024819.
38. SCRATCH Protein Predictor. 2009, , http://scratch.proteomics.ics.uci.edu/
39. Arvidsson S, Kwasniewski M, Riano-Pachón DM, Mueller-Roeber B. QuantPrime -- a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics 2008, 9:465. 10.1186/1471-2105-9-465, 2612009, 18976492.
40. Lassmann T, Sonnhammer E. Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinformatics 2007, 8(Suppl 5):S9. 10.1186/1471-2105-8-S5-S9, 1892097, 17570868.