dms_tools specifications

Information


Unique identifier OMICS_08947
Name dms_tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Weblogo, pystan
Maintained Yes

Versioning


Add your version

Documentation


Publication for dms_tools

dms_tools in publications

 (9)
PMCID: 5895760
PMID: 29643370
DOI: 10.1038/s41467-018-03665-3

[…] rs and sampling statistics are in the methods section. open-source software that performs all steps in the analysis beginning with the deep sequencing data is available at https://jbloomlab.github.io/dms_tools2/., we applied this approach to anti-ha antibodies with a range of breadths and epitopes. the crystal structures or sites of escape mutations selected by these antibodies are shown in fig. . […]

PMCID: 5910023
PMID: 29590010
DOI: 10.7554/eLife.34420.047

[…] only summarizes one aspect of the deep mutational scanning data, but and contain detailed plots showing all aspects of the data (read depth, per-site mutation rate, etc) as generated by the dms_tools2 software (, https://jbloomlab.github.io/dms_tools2/)., 10.7554/elife.34420.012 figure 3—figure supplement 1. , we used the deep mutational scanning data to estimate the preference […]

PMCID: 5715146
PMID: 29203891
DOI: 10.1038/s41598-017-17081-y

[…] zymoclean column. sequencing was performed on a nextseq. 500 with a mid output kit v2 (illumina) using 2 × 150 bp paired end reads., in order to get nucleotide counts from subamplicon sequence data, dms_tools version 1.1.3 was modified to include a nucleotide counting feature in dms_barcodedsubamplicons. the count files generated as output were then combined into a large dataframe with added […]

PMCID: 5383324
PMID: 28346537
DOI: 10.1371/journal.ppat.1006288

[…] expressing the inactive t103a mxa to those in the non-expressing cells., computer programs to calculate the differential selection values and display them in logo plots were implemented into the dms_tools software [] available at https://github.com/jbloomlab/dms_tools. we used version 1.1.17 of this software for the analyses in this paper., we measured polymerase activity for different np […]

PMCID: 5363992
PMID: 28288189
DOI: 10.1371/journal.ppat.1006271

[…] hiseq2500 using 2 x 250 bp paired-end reads in rapid-run mode. provides summary statistics of the deep sequencing libraries., the frequency of each mutation in each sample was determined by using dms_tools [] (http://jbloomlab.github.io/dms_tools/), version 1.1.20, to align subamplicon reads to a reference ha sequence, group barcodes to build consensus sequences, and quantify mutation counts […]


To access a full list of publications, you will need to upgrade to our premium service.

dms_tools institution(s)
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

dms_tools reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review dms_tools