Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from https://pubmed.ncbi.nlm.nih.gov/23329690/ below:

MAFFT multiple sequence alignment software version 7: improvements in performance and usability

Affiliations

• ¹ Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan. kazutaka.katoh@aist.go.jp

• PMID: 23329690
• PMCID: PMC3603318
• DOI: 10.1093/molbev/mst010

Item in Clipboard

Kazutaka Katoh et al. Mol Biol Evol. 2013 Apr.

• ¹ Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan. kazutaka.katoh@aist.go.jp

• PMID: 23329690
• PMCID: PMC3603318
• DOI: 10.1093/molbev/mst010

Item in Clipboard

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.

PubMed Disclaimer

Assumptions on the phylogenetic relationship…

Assumptions on the phylogenetic relationship in different options of MAFFT. ( A )…

Assumptions on the phylogenetic relationship in different options of MAFFT. (A) mafft-profile , (B) –– addprofile , (C), misuse of mafft-profile , and (D) –– add or –– addprofile .

ITS alignments by different options…

ITS alignments by different options of MAFFT, displayed on Jalview (Waterhouse et al.…

ITS alignments by different options of MAFFT, displayed on Jalview (Waterhouse et al. 2009). (A, B) Incorrect alignments by the FFT-NS-2 and L-INS-i algorithms, respectively. (C) An incorrect alignment by mafft-profile . The full-length sequences were aligned with the L-INS-i algorithm and then each new sequence was separately added to the full-length alignment, using mafft-profile . (D) Reasonable alignment by a two-step strategy. The –– 6merpair –– addfragments option was used at the second step. (E) Reordered version of D; sequences are ordered such that similar sequences are placed closely. All calculations were performed using 16 cores on a Linux PC with 2.67 GHz Intel Xeon E7-8837/256 GB RAM.

( A ) A part…

( A ) A part of output of the –– treeout option showing…

(A) A part of output of the –– treeout option showing the phylogenetic positions of new sequences ( new# ) in the tree of the existing alignment ( backbone# ), estimated before the alignment calculation. This file also shows a Newick format tree of the existing alignment (not shown in this figure). For each new sequence, the nearest sequence in the existing alignment ( nearest sequence ), approximate distance to the nearest sequence ( approximate distance ), and the members of the sister group ( sister group ) are shown. (B) Graphical representation of (A).

( A ) Superposition of…

( A ) Superposition of 3v33, 2qip, and 1taq structures visualized by PyMOL…

(A) Superposition of 3v33, 2qip, and 1taq structures visualized by PyMOL (Schrödinger LLC 2010). (B) MAFFT-L-INS-i sequence alignment displayed on jalview (Waterhouse et al. 2009). Misaligned Ds are highlighed in red. (C) Structure-informed MSA with correctly aligned Ds; Alpha helices and beta sheets are shown in blue and yellow, respectively, in (A–C).

• Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma.

  Liao X, Xie D, Bao T, Hou M, Li C, Nie B, Sun S, Peng D, Hu H, Wang H, Tao Y, Zhang Y, Li W, Wang L. Liao X, et al. Nat Commun. 2024 Oct 29;15(1):9349. doi: 10.1038/s41467-024-53719-y. Nat Commun. 2024. PMID: 39472560 Free PMC article.

• AAVolve: Concatenated long-read deep sequencing enables whole capsid tracking during shuffled AAV library selection.

  Scott S, Westhaus A, Nazareth D, Cabanes-Creus M, Navarro RG, Chandra D, Zhu E, Venkateswaran A, Alexander IE, Bauer DC, Wilson LOW, Lisowski L. Scott S, et al. Mol Ther Methods Clin Dev. 2024 Oct 4;32(4):101351. doi: 10.1016/j.omtm.2024.101351. eCollection 2024 Dec 12. Mol Ther Methods Clin Dev. 2024. PMID: 39498467 Free PMC article.

• Exploring Dengue Infection in a Vaccinated Individual: Preliminary Molecular Diagnosis and Sequencing Insights.

  Adelino TÉR, Pedroso SHSP, Lima M, Tomé LMR, Guimarães NR, Fonseca V, Silva PESD, Moreno KMF, Silva ACAE, Pinheiro NR, Souza CSA, Alcantara LCJ, Giovanetti M, Iani FCM. Adelino TÉR, et al. Viruses. 2024 Oct 12;16(10):1603. doi: 10.3390/v16101603. Viruses. 2024. PMID: 39459936 Free PMC article.

1. 1. Altschul SF. Generalized affine gap costs for protein sequence alignment. Proteins. 1998;32:88–96. - PubMed
2. 1. 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. - PubMed
3. 1. Berger MP, Munson PJ. A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci. 1991;7:479–484. - PubMed
4. 1. Berger SA, Stamatakis A. Aligning short reads to reference alignments and trees. Bioinformatics. 2011;27:2068–2075. - PubMed
5. 1. Blackburne BP, Whelan S. Class of multiple sequence alignment algorithm affects genomic analysis. Mol Biol Evol. 2012a Advance access published December 4, 2012, doi:10.1093/molbev/mss256. - PubMed

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.3