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+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
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+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
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+
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+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ {signature of Ty Coon}, 1 April 1989
+ Ty Coon, President of Vice
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+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
+
+
+ Drost H, Gogleva A (2022). +
Drost H, Gogleva A (2023). metablastr: Perform Massive Local BLAST Searches. -R package version 0.3.1, https://github.com/drostlab/metablastr. +R package version 0.3.2, https://github.com/drostlab/metablastr.
@Manual{,
title = {metablastr: Perform Massive Local BLAST Searches},
author = {Hajk-Georg Drost and Anna Gogleva},
- year = {2022},
- note = {R package version 0.3.1},
+ year = {2023},
+ note = {R package version 0.3.2},
url = {https://github.com/drostlab/metablastr},
}
@@ -88,7 +88,7 @@ The exponentially growing number of available sequences in biological databases revolutionizes the way modern life science research is conducted. Approximately hundred thousand genomic sequences spanning diverse species from the tree of life are currently publically available and free to access. It is now possible to access and retrieve this data automatically using the R package biomartr and the next step is to harness this wealth of sequence diversity to explore and detect novel patterns of evolvability, variation, and disease emergence.
-The R package biomartr solves the problem of retrieving this vast amount of biological sequence data in a standardized and computationally reproducible way and the metablastr package aims to solve the problem of performing massive scale sequence searches in a standardized and computationally reproducible way.
Both packages, biomartr and metablastr are designed to complement each other seamlessly to provide users with a toolset to automatically retrieve thousands of biological sequences (thousands of genomes, proteomes, annotations, etc) and to use these sequences to perform massive sequence searches with BLAST to extract novel patterns of similarity and divergence between large sets of species.
The most prominent tool to perform sequence searches at scale is the Basic Local Alignment Search Tool (BLAST) which is designed to find regions of sequence similarity between query and a subject sequences or sequence databases.
+With the rapid expansion of available sequences in biological databases, the landscape of modern life science research is being transformed. Currently, around several hundred thousand genomic sequences from a diverse array of species in the tree of life are freely accessible to the public. The R package biomartr enables automated access and retrieval of this vast data, paving the way to delve into the rich tapestry of sequence diversity, uncovering new insights into evolvability, variation, and the emergence of diseases.
+The biomartr package streamlines the retrieval of a massive amount of biological sequence data in a standardized and reproducible manner. Complementing it, the metablastr package is tailored to facilitate large-scale sequence searches, also in a standardized and reproducible approach.
In synergy, biomartr and metablastr provide researchers with a comprehensive toolset, allowing them to efficiently gather thousands of biological sequences (genomes, proteomes, annotations, etc.) and conduct extensive sequence comparisons using the gold standard sequence search engine BLAST. This facilitates the extraction of novel patterns highlighting similarities and divergences among vast sets of species.
It’s worth noting that the go-to instrument for large-scale sequence searches is BLAST (Basic Local Alignment Search Tool). It is purposefully built to identify regions of sequence similarity between a given query and subject sequences or sequence databases.
+Building on these advancements, we have recently introduced DIAMOND2, a groundbreaking software solution designed to accelerate BLAST searches by an factor of up to 10,000x. To offer researchers even more flexibility and integration, we provide rdiamond, a dedicated interface package that allows programmatic handling of DIAMOND2 sequence searches directly through R. This not only streamlines the sequence search process but also ensures that researchers can access and utilize the power of DIAMOND2 within a familiar R environment.
The metablastr package is still under development and not formally published yet. However, we did develop parts of metablastr for this Methods chapter which you can cite until a metablastr specific manuscript is prepared.
+M Benoit, HG Drost. A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. In: Cho J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY (2021).
+M Benoit, HG Drost. A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants. In: Cho J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY (2021).
+
metablastr by typing
-if (!requireNamespace("BiocManager", quietly = TRUE))
+# install BiocManager if required
+if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
-BiocManager::install()
+BiocManager::install()
-BiocManager::install(c("Biostrings", "GenomicFeatures", "GenomicRanges", "Rsamtools", "IRanges", "rtracklayer", "biomaRt"))
+# install package dependencies
+BiocManager::install(
+ c(
+ "Biostrings",
+ "GenomicFeatures",
+ "GenomicRanges",
+ "Rsamtools",
+ "IRanges",
+ "rtracklayer")
+)
# install.packages("devtools")
# install the current version of metablastr on your system
-devtools::install_github("HajkD/metablastr", build_vignettes = TRUE, dependencies = TRUE)Please follow the Installation Vignette to install all standalone sequence search tools.
metablastr:
@@ -231,14 +246,18 @@ filter_blast_:filter_blast_:list_outformats(): List available BLAST output formatslist_outformats(): List available BLAST output formatsa value passed to aes specifying the transparency of distributions.
a value passed to aes specifying the transparency of distributions.
the ridges scale passed to geom_density_ridges.
the ridges scale passed to geom_density_ridges.
a character vector specifying the exact order of species names (levels)
-that is used to factor and sort species in the geom_density_ridges plot.
factor and sort species in the geom_density_ridges plot.
a value passed to aes specifying the transparency of distributions.
a value passed to aes specifying the transparency of distributions.
the ridges scale passed to geom_density_ridges.
the ridges scale passed to geom_density_ridges.
a character vector specifying the exact order of species names (levels)
-that is used to factor and sort species in the geom_density_ridges plot.
factor and sort species in the geom_density_ridges plot.