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Belvu specifications

Information


Unique identifier OMICS_23184
Name Belvu
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format STOCKHOLM,MSF,SELEX,FASTA
Output format STOCKHOLM,MSF,SELEX,FASTA
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Version 4.14
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Gemma Barson <>

Additional information


http://www.sanger.ac.uk/science/tools/seqtools

Publications for Belvu

Belvu in pipelines

 (7)
2017
PMCID: 5457479
PMID: 28502659
DOI: 10.1016/j.cub.2017.04.023

[…] sample size. statistical analysis was performed using the prism 6.0 software., alignments were produced with t-coffee [], using default parameters, slightly refined manually and viewed with the belvu program []. profiles of the alignments, as global hidden markov models (hmms), were generated using hmmer2 []. homologous protein sequences were identified by iterative similarity searches […]

2016
PMCID: 4759884
PMID: 26891798
DOI: 10.1186/s12915-016-0228-7

[…] (hmmer2.0) []. the alignment was converted from stockholm to fasta format using bioscripts.convert tools v0.4 (https://pypi.python.org/pypi/bioscripts.convert/0.4). the alignment was examined with belvu program and trimmed to the domain borders. trimmed sequences were then re-aligned with muscle []., the evolution of tir_2 domains was inferred with mega5 [] using the maximum likelihood method […]

2015
PMCID: 4432964
PMID: 25924720
DOI: 10.1186/s13059-015-0655-8

[…] and homologous sequences from a jackhmmer search []. a non-redundant set of sequences of 90% identity or less was aligned with mafft [] with default settings. alignments were visualised with belvu [] and phylogenetic trees constructed using the neighbour-joining method present in belvu using default parameters., additional file 1: , competing interests , the authors declare […]

2014
PMCID: 4263179
PMID: 25566323
DOI: 10.3389/fgene.2014.00439

[…] for each expera domain-containing families were generated independently with the program t-coffee using default parameters (notredame et al., ), slightly refined manually and visualized with the belvu program (sonnhammer and hollich, ). profiles of the alignment as global hidden markov models (hmms) were generated using hmmer (eddy, ; finn et al., ). profile-based sequence searches […]

2012
PMCID: 3511201
PMID: 22929533
DOI: 10.1186/1479-5876-10-174

[…] nearest neighbor sequence from rdp was recruited into the alignment per input sequence. the alignment was downloaded and trimmed to remove columns whose gap fractions were greater than 50%, using belvu []. based on the alignment, a bootstrapped neighbor-joining (nj) tree was subsequently inferred using paupfasta, an in-house wrapper script around the paup* program as described [], and edited […]


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Belvu in publications

 (17)
PMCID: 5940140
PMID: 29559535
DOI: 10.1534/g3.118.200257

[…] annotations were merged from entap to further characterize the results., multiple sequence alignments of each conserved gene family were prepared with muscle (). alignments were evaluated in belvu by conservation scores and those with excessive gaps and missing data were filtered (). pairwise alignments across all four species were evaluated with codeml (paml, v.4.6) (). the tree file […]

PMCID: 5290159
PMID: 28128207
DOI: 10.1038/ncomms14246

[…] >0.0001), bit score >50, and length (only those >75% length were kept), and further aligned by mafft [ http://mafft.cbrc.jp/alignment/software/]. the alignments were visualized with belvu [ http://sonnhammer.sbc.su.se/belvu.html] to check for quality. we removed the redundancy of the alignment discarding sequences with more than 63% of sequence identity. we next generated markov […]

PMCID: 5087659
PMID: 27587838
DOI: 10.1242/jcs.193375

[…] were performed with psipred ()., protein amino acid sequences were obtained from uniprot or dictybase (; ). alignments of protein sequences were performed using muscle or t-coffee, and visualised in belvu (; ; ). dna sequences were aligned using the multalin interface ()., gst-tagged proteins were generated by amplifying the following regions of the apl gene from cdna and ligation into pgex-4t-1 […]

PMCID: 4742741
PMID: 26668325
DOI: 10.1074/jbc.M115.685222

[…] of each tldc gene was compared with the mean ct value for c20orf118., alignments were produced with t-coffee () using default parameters and refined manually. protein alignments are presented using belvu () with a coloring scheme indicating the average blosum62 scores (which are correlated with amino acid conservation) of each alignment column: red (>3.5), purple (between 3.5 and 2), […]

PMCID: 4462073
PMID: 26058375
DOI: 10.1186/s12862-015-0378-1

[…] training set of sequences with the hmm the hmmscore program was used. alignments of the hits were performed with the program align2model [], and editions and redundancy analyses were performed with belvu alignment viewer []. the best ten hits were aligned to the hmm as above, and the hits of the original entries were removed from the initial training set to avoid re-sampling in the following […]


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Belvu institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Belvu funding source(s)
Supported by the Wellcome Trust Grant (098051); and the National Human Genome Research Institute Grant (5U54HG00455-04).

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