Selected article for: "MAFFT program and multiple sequence alignment"
Author: Masaki Tagashira
Title: PhyloFold: Precise and Swift Prediction of RNA Secondary Structures to Incorporate Phylogeny among Homologs
  • Document date: 2020_3_6
    • ID: l72x4wn3_31
    Snippet: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights . https://doi.org/10.1101/2020.03.05.975797 doi: bioRxiv preprint (Katoh and Standley, 2013) were used to compute the sequence alignments to input into the PhyloAliFold program. The MAFFT G-INS-i executes only classic multiple sequence alignment whereas the MAFFT X-INS-i considers structural alignments during multiple sequence alignment to decomp.....
    Document: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights . https://doi.org/10.1101/2020.03.05.975797 doi: bioRxiv preprint (Katoh and Standley, 2013) were used to compute the sequence alignments to input into the PhyloAliFold program. The MAFFT G-INS-i executes only classic multiple sequence alignment whereas the MAFFT X-INS-i considers structural alignments during multiple sequence alignment to decompose them. The reference sequence alignments of the ncRNA families in test set "aligned" are also used as the input of the PhyloAliFold. Table 4 . The benchmark of γ-dependent programs that predict single secondary structures on running time using test set "unaligned".

    Search related documents:
    Co phrase search for related documents
    • decompose alignment and secondary structure: 1
    • decompose alignment and sequence alignment: 1
    • decompose alignment and structural alignment: 1
    • multiple sequence alignment and reference sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14
    • multiple sequence alignment and reference sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9
    • multiple sequence alignment and secondary structure: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
    • multiple sequence alignment and sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • multiple sequence and reference sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
    • multiple sequence and reference sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9
    • multiple sequence and secondary structure: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21
    • multiple sequence and sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • ncRNA family and secondary structure: 1
    • ncRNA family and sequence alignment: 1
    • reference sequence alignment and sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • reference sequence and run time: 1
    • reference sequence and secondary structure: 1, 2, 3, 4, 5
    • reference sequence and sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • secondary structure and single secondary structure: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18
    • secondary structure and single secondary structure predict: 1, 2, 3