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OXBench specifications


Unique identifier OMICS_00983
Name OXBench
Restrictions to use None
Maintained Yes

Publication for OXBench

OXBench citations


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

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 total length. It includes five diverse referen […]


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

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

[…] ide trees. For 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 scor […]


A simple method to control over alignment in the MAFFT multiple sequence alignment program

PMCID: 4920119
PMID: 27153688
DOI: 10.1093/bioinformatics/btw108

[…] od, MAFFT-FFT-NS-2, and MAFFT-G-INS-i with the - - leavegappyregion option (used in ) were included in the comparison as reference.The results of two different protein-based benchmarks, PREFAB () and OXBench (), are shown in . These datasets are based on protein structural alignments. In relatively difficult cases, only short conserved regions (usually functional sites under strong evolutionary co […]


Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

PLoS One
PMCID: 4438059
PMID: 25993129
DOI: 10.1371/journal.pone.0127431

[…] roduce trusted reference alignments []. As already mentioned, these reference alignments are normally obtained from a manually (or semi-automatically) curated alignment database, such as BAliBASE [], OXBENCH [], PREFAB [], or SABmark []. It has been shown that in addition to the divergence of the sequences, the performance of an MSA method depends also on several other factors such as sequence len […]


Improving multiple sequence alignment by using better guide trees

BMC Bioinformatics
PMCID: 4402577
PMID: 25859903
DOI: 10.1186/1471-2105-16-S5-S4

[…] fied GLProbs to GLProbs-Random, which replaces the guide tree constructed in GLProbs by a random guide tree. We have used them to align protein sequences families obtained from the benchmark database OXBench. Figure shows their alignments' sum-of-pairs (SP) scores and total column (TC) scores, two of the most commonly used scores for measuring the quality of MSA. Each dot (x, y) in the figure sho […]


How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

BMC Genomics
PMCID: 3303716
PMID: 22759650
DOI: 10.1186/1471-2164-13-S4-S2

[…] ics there are benchmarks e.g. for multiple sequence alignment methods already 1990’s []. Novel MSA construction methods are routinely tested with alignment benchmarks such as BAliBASE [] HOMSTRAD [], OxBench suite [], PREFAB [], and SABmark [] . Other bioinformatic benchmarks include protein 3D structure prediction [-], protein structure and function prediction [], protein-protein docking [] and g […]

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OXBench institution(s)
School of Life Sciences, University of Dundee, Dow St, Dundee, Scotland, UK

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