Literature DB >> 25564671

Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments.

Kieran Boyce1, Fabian Sievers1, Desmond G Higgins2.   

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Year:  2015        PMID： 25564671      PMCID： PMC4299201          DOI： 10.1073/pnas.1419351112

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  5 in total

1.  Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.

Authors:  Mike S S Chang; Steven A Benner
Journal:  J Mol Biol       Date:  2004-08-06       Impact factor: 5.469

2.  Analysis of insertions/deletions in protein structures.

Authors:  S Pascarella; P Argos
Journal:  J Mol Biol       Date:  1992-03-20       Impact factor: 5.469

3.  Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

Authors:  Ge Tan; Manuel Gil; Ari P Löytynoja; Nick Goldman; Christophe Dessimoz
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-06       Impact factor: 11.205

4.  Simple chained guide trees give high-quality protein multiple sequence alignments.

Authors:  Kieran Boyce; Fabian Sievers; Desmond G Higgins
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-07       Impact factor: 11.205

5.  Systematic exploration of guide-tree topology effects for small protein alignments.

Authors:  Fabian Sievers; Graham M Hughes; Desmond G Higgins
Journal:  BMC Bioinformatics       Date:  2014-10-04       Impact factor: 3.169
  5 in total
  6 in total

1.  Protein multiple sequence alignment benchmarking through secondary structure prediction.

Authors:  Quan Le; Fabian Sievers; Desmond G Higgins
Journal:  Bioinformatics       Date:  2017-05-01       Impact factor: 6.937

2.  QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families.

Authors:  Adam Gudyś; Sebastian Deorowicz
Journal:  Sci Rep       Date:  2017-01-31       Impact factor: 4.379

Review 3.  Developments in Algorithms for Sequence Alignment: A Review.

Authors:  Jiannan Chao; Furong Tang; Lei Xu
Journal:  Biomolecules       Date:  2022-04-06

4.  DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.

Authors:  Erik S Wright
Journal:  BMC Bioinformatics       Date:  2015-10-06       Impact factor: 3.169

5.  FAMSA: Fast and accurate multiple sequence alignment of huge protein families.

Authors:  Sebastian Deorowicz; Agnieszka Debudaj-Grabysz; Adam Gudyś
Journal:  Sci Rep       Date:  2016-09-27       Impact factor: 4.379

6.  Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments.

Authors:  Gearóid Fox; Fabian Sievers; Desmond G Higgins
Journal:  Bioinformatics       Date:  2015-11-14       Impact factor: 6.937
  6 in total

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