OXBench

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]