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BAliBASE specifications

Information


Unique identifier OMICS_00971
Name BAliBASE
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Olivier Poch

Publications for BAliBASE

BAliBASE citations

 (66)
library_books

Disease Sequences High Accuracy Alignment Based on the Precision Medicine

2018
Biomed Res Int
PMCID: 5842723
PMID: 29682519
DOI: 10.1155/2018/1718046

[…] work to determine the optimum parameters. The current parameters pertaining to the objective function in most literature are empirical values which are independently associated with the sequences []. BALiBASE is a database of manually refined multiple sequence alignments [] and is usually used to test performance of MSA method [].Many open source online alignment tools are available that can align […]

library_books

Bacterial Foraging Optimization –Genetic Algorithm for Multiple Sequence Alignment with Multi Objectives

2017
Sci Rep
PMCID: 5562892
PMID: 28821841
DOI: 10.1038/s41598-017-09499-1

[…] In this work the universally known benchmark datasets such as Benchmark Alignment Database (BAliBASE 3.0), Prefab 4.0, SABmark 1.65 and Oxbench 1.3 is used to examine and compare with various multiple sequence alignment methods. The BAliBASE 3.0 database contains 6255 protein sequences in to […]

library_books

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

2017
Sci Rep
PMCID: 5282490
PMID: 28139687
DOI: 10.1038/srep41553

[…] nnet160 matrix for partition function calculation by VTML200, which was proven to be more accurate. This was followed by training partition function parameters, i.e., gap penalties and temperature on BAliBASE 3 benchmark with a use of NOMAD algorithm for optimization of non-smooth functions. Another changes were introduced in order to shorten execution time. They include redesigning graphics proce […]

library_books

IBBOMSA: An Improved Biogeography based Approach for Multiple Sequence Alignment

2016
Evol Bioinform Online
PMCID: 5084829
PMID: 27812276
DOI: 10.4137/EBO.S40457

[…] algorithms such as MSAProbs, Probalign, MAFFT, Procons, Clustal Omega, T-Coffee, Kalign, MUSCLE, FSA, DIALIGN, PRANK, and CLUSTALW. shows the average TC scores of these algorithms on six subsets of BAliBASE 3.0. The data used in are drawn from Ref. , except the data about IBBOMSA. The proposed IBBOMSA is the fourth best aligner in terms of accuracy. The top aligners are MSAProbs, which reach th […]

call_split

PnpProbs: a better multiple sequence alignment tool by better handling of guide trees

2016
BMC Bioinformatics
PMCID: 5009527
PMID: 27585754
DOI: 10.1186/s12859-016-1121-7
call_split See protocol

[…] or ease of reference, we use GLProbs-UPGMA to refer the original GLProbs, and GLProb-WPGMA to refer the modified one. We used both tools to align the normally related families in SABmark, OXBench and BALiBASE, and compute the TC scores of the resulting alignments, which is one of the most commonly used performance measure for evaluating multiple sequence alignments; the higher the scores, the bett […]

call_split

LEON BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system

2016
BMC Bioinformatics
PMCID: 4936259
PMID: 27387560
DOI: 10.1186/s12859-016-1146-y
call_split See protocol

[…] To test the performance of the program, we used the most recent test set (Reference 10) in the BAliBASE benchmark suite [], composed of 218 reference alignments and containing a total of 17,892 protein sequences. These reference alignments are designed to reflect some of the problems specific t […]

Citations

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BAliBASE institution(s)
Departement de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France; Genome Center and Department of Computer Science, University of California, Davis, CA, USA
BAliBASE funding source(s)
This project was funded by the Institut National de la Sante et de la Recherche Médicale; the Centre National de la Recherche Scientifique; the Hopital Universitaire de Strasbourg; the Fond National de la Science (GENOPOLE) and the SPINE project grant No. QLG2-CT-2002-00988.

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