publication . Other literature type . Article . 2013

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Standley, Daron M.; Katoh, Kazutaka;
  • Published: 16 Jan 2013
  • Publisher: Oxford University Press (OUP)
Abstract
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Subjects
free text keywords: Fast Tracks, multiple sequence alignment, metagemone, protein structure, progressive alignment, parallel processing, Genetics, Biology, Software versioning, Plastid Genomes, Usability, business.industry, business, Software
48 references, page 1 of 4

Altschul, SF. Generalized affine gap costs for protein sequence alignment. Proteins. 1998; 32: 88-96 [OpenAIRE] [PubMed]

Barton, GJ, Sternberg, MJ. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol.. 1987; 198: 327-337 [OpenAIRE] [PubMed]

Berger, MP, Munson, PJ. A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci.. 1991; 7: 479-484 [OpenAIRE] [PubMed]

Berger, SA, Stamatakis, A. Aligning short reads to reference alignments and trees. Bioinformatics. 2011; 27: 2068-2075 [PubMed]

Blackburne, BP, Whelan, S. Class of multiple sequence alignment algorithm affects genomic analysis. Mol Biol Evol.. 2012a [OpenAIRE]

Blackburne, BP, Whelan, S. Measuring the distance between multiple sequence alignments. Bioinformatics. 2012b; 28: 495-502 [PubMed]

Cannone, JJ, Subramanian, S, Schnare, MN. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002; 3: 2 [OpenAIRE] [PubMed]

Cole, JR, Wang, Q, Cardenas, E. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res.. 2009; 37: D141-D145 [OpenAIRE] [PubMed]

Dessimoz, C, Gil, M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol.. 2010; 11: R37 [OpenAIRE] [PubMed]

Feng, DF, Doolittle, RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol.. 1987; 25: 351-360 [OpenAIRE] [PubMed]

Fletcher, W, Yang, Z. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol.. 2009; 26: 1879-1888 [OpenAIRE] [PubMed]

Golubchik, T, Wise, MJ, Easteal, S, Jermiin, LS. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. Mol Biol Evol.. 2007; 24: 2433-2442 [OpenAIRE] [PubMed]

Gotoh, O. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci.. 1993; 9: 361-370 [PubMed]

Gotoh, O. A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci.. 1995; 11: 543-551 [PubMed]

Henikoff, S, Henikoff, JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A.. 1992; 89: 10915-10919 [OpenAIRE] [PubMed]

48 references, page 1 of 4
Abstract
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Subjects
free text keywords: Fast Tracks, multiple sequence alignment, metagemone, protein structure, progressive alignment, parallel processing, Genetics, Biology, Software versioning, Plastid Genomes, Usability, business.industry, business, Software
48 references, page 1 of 4

Altschul, SF. Generalized affine gap costs for protein sequence alignment. Proteins. 1998; 32: 88-96 [OpenAIRE] [PubMed]

Barton, GJ, Sternberg, MJ. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol.. 1987; 198: 327-337 [OpenAIRE] [PubMed]

Berger, MP, Munson, PJ. A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci.. 1991; 7: 479-484 [OpenAIRE] [PubMed]

Berger, SA, Stamatakis, A. Aligning short reads to reference alignments and trees. Bioinformatics. 2011; 27: 2068-2075 [PubMed]

Blackburne, BP, Whelan, S. Class of multiple sequence alignment algorithm affects genomic analysis. Mol Biol Evol.. 2012a [OpenAIRE]

Blackburne, BP, Whelan, S. Measuring the distance between multiple sequence alignments. Bioinformatics. 2012b; 28: 495-502 [PubMed]

Cannone, JJ, Subramanian, S, Schnare, MN. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002; 3: 2 [OpenAIRE] [PubMed]

Cole, JR, Wang, Q, Cardenas, E. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res.. 2009; 37: D141-D145 [OpenAIRE] [PubMed]

Dessimoz, C, Gil, M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol.. 2010; 11: R37 [OpenAIRE] [PubMed]

Feng, DF, Doolittle, RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol.. 1987; 25: 351-360 [OpenAIRE] [PubMed]

Fletcher, W, Yang, Z. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol.. 2009; 26: 1879-1888 [OpenAIRE] [PubMed]

Golubchik, T, Wise, MJ, Easteal, S, Jermiin, LS. Mind the gaps: evidence of bias in estimates of multiple sequence alignments. Mol Biol Evol.. 2007; 24: 2433-2442 [OpenAIRE] [PubMed]

Gotoh, O. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci.. 1993; 9: 361-370 [PubMed]

Gotoh, O. A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci.. 1995; 11: 543-551 [PubMed]

Henikoff, S, Henikoff, JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A.. 1992; 89: 10915-10919 [OpenAIRE] [PubMed]

48 references, page 1 of 4
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publication . Other literature type . Article . 2013

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Standley, Daron M.; Katoh, Kazutaka;