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PIBASE specifications


Unique identifier OMICS_02956
Restrictions to use None
Maintained Yes

Publication for PIBASE

PIBASE citations


Identification and characterization of two functional variants in the human longevity gene FOXO3

Nat Commun
PMCID: 5727304
PMID: 29234056
DOI: 10.1038/s41467-017-02183-y

[…] rge.net/), variant calling was performed with SAMtools and GATK, and the results were subsequently merged for further analysis using GATK’s CombineVariants. False-positive SNV calls were removed with pibase and annotation was performed with an in-house pipeline.In another set of 138 LLI (mean age: 101.5 years) and 92 controls (60–75 years), Sanger sequencing (Thermo Fisher Scientific, Waltham, Mas […]


Composition of Overlapping Protein Protein and Protein Ligand Interfaces

PLoS One
PMCID: 4627654
PMID: 26517868
DOI: 10.1371/journal.pone.0140965

[…] tics, see e.g. [,–]. Comparing these features of protein interfaces to those of overlapping protein-ligand interfaces should aid in targeting protein-protein interaction sites. Here, we used the ABC, PIBASE and Timbal databases as data sources for protein interfaces and surfaces. All three databases are secondary database that are derived from the PDB. However, due to the different way of identify […]


Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing

PLoS One
PMCID: 3883664
PMID: 24409309
DOI: 10.1371/journal.pone.0084785

[…] n the coding region most bioinformatic pipelines do find mutations by comparing sequencing of both tumor and normal tissue. There are bioinformatic tools to deal with these issues like VarScan 2 and pibase , but this might have the limitation of only studying high quality regions.RNA-sequencing (RNA-seq) could potentially be useful for validating mutations identified in WGA sequence data. On aver […]


From next generation sequencing alignments to accurate comparison and validation of single nucleotide variants: the pibase software

Nucleic Acids Res
PMCID: 3592472
PMID: 22965131
DOI: 10.1093/nar/gks836
call_split See protocol

[…] For our example data download on the project homepage (http://www.ikmb.uni-kiel.de/pibase, 23 August 2012, date last accessed), we used the publicly available BAM files for chromosome 22, (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/pilot2_high_cov_GRCh37_bams/, 23 August 201 […]


Improving mapping and SNP calling performance in multiplexed targeted next generation sequencing

BMC Genomics
PMCID: 3563481
PMID: 22913592
DOI: 10.1186/1471-2164-13-417

[…] y region’) and codes ‘h4, h10, h9’ for rs206123 (‘too many invalid dicolors found, no conclusive second allele found, tri-allelic SNP’). We therefore complemented our analysis with CLC bio, NextGENe, pibase and IGV. We streamlined our manual genotype calling in IGV by classifying a genotype as homozygous if more than 80% of the reads indicated the same base at that position. Otherwise we classifie […]


Structural Modeling of Protein Interactions by Analogy: Application to PSD 95

PLoS Comput Biol
PMCID: 1635541
PMID: 17096593
DOI: 10.1371/journal.pcbi.0020153

[…] Comparative patch analysis application. Comparative patch analysis was used to predict the tertiary structure of the rat PSD-95 core fragment that contains the PDZ3, SH3, and GK domains. From PIBASE, 126, 298, and 517 protein binding sites were obtained for the PDZ3, SH3, and GK domains, respectively. The binding sites were mapped onto the target structures. Redundant binding sites were re […]


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PIBASE institution(s)
Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, USA

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