biodata === BioData is a Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics. Its aim is to keep applications as agnostic as possible from the file formats they receive as input. This way, analysis can be conducted...
BMC Bioinformatics (2019) 20:402 https://doi.org/10.1186/s12859-019-2982-3 SOFTWARE JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface Ben C. Stöver* , Sarah Wiechers and Kai F. Müller Open Access Abstract Back...
BackgroundToday a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representation. Although most currently available software only supports the classical formats ...
Since there are no benefits in acquiring low-quality, unidentifiable spectra, and there are potential drawbacks (additional storage and perhaps additional data filtering required, depending on the bioinformatics pipeline), we conclude that a threshold value set at or very close below the noise level ...
Source data are provided as a Source Data file. Full size image This transcriptomic analysis suggests that single cells within the organoids might display differences in mechanical phenotype as a function of their LGR5 expression. To test this possibility, we dissociated single cells from the ...
taken from the 43 sites. More information about the samples can be found in Additional file1: Table S1.eIn situ ecosystem-level nitrous oxide (N2O) and methane (CH4) fluxes measured from the 43 sites using a static, non-steady state, non-flow-through system. Negative values represent net ...
These can be found at the UCSC Genome Bioinformatics Downloads Page, by following the "liftOver" links for your organism of choice. Change Log liftOverPlink is modified from the liftMap.py script provided by the Abecasis Lab to: Take a user specified chain file. To look for liftOver in $...
Databases have non-biological redundancy This is problematic when training data- driven prediction methods –As you saw for PSSM construction Uniprot has a feature to remove redundancy (90% or 50%). How is this done? This and much more you will find out in the next episode of......
Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World ca
In biochemistry there are strict laboratory protocols that ensure reproducibility of the analytical methods, while in bioinformatics this function is accomplished by implementing reusable computational workflows7,8. Thus, in addition to the dataset we also address the typical bioinformatic challenges that co...