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A suite of software tools will be required to convert sequence data into a format that is relevant and useful for clinicians and infection control teams.
We have developed a number of tools in the Perl scripting language to convert sequence and annotation data into a format accepted by JBrowse (version 1.11.1), which are included as Additional files 1, 2 and 3.
Because rates of molecular evolution can vary across taxa [ 36], we did not convert sequence divergence values provided in original articles into diversification dates using a standard molecular clock (e.g., 2%; [ 3]).
It is often traditionally assumed that both cis-regulatory and coding DNA are inert with respect to the information they carry, wholly dependent upon interactions with complex protein-based systems designed to convert sequence information into cell functions.
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Neighbor Joining trees of H. pylori from selected populations were created by Molecular Evolutionary Genetics Analysis (MEGA, version 3.1; http://www.megasoftware.net/); the DNA sequence polymorphism (DnaSP, http://www.ub.es/dnasp/) program was used to convert sequences from Fasta to Mega format.
The oligonucleotides are easier to generate for local mutagenesis but obviously cannot convert sequences over a long distance.
Results: In this article, we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations.
These functions are useful for converting sequence into a canonical form suitable for representing a set.
The GV of each enhanced sequence is increased up to the level where the MCD between the converted sequence and its enhanced version reaches a preset threshold value, denoted as θ MCD.
Probe sequences the size of 25 nucleotides were synthesized, resembling the sodium bisulfite converted sequence of each CGI of interest.
However, unlike the previous example, the converting sequence does not appear to be the native P. macrorhiza atp1 gene.
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