Search Results for "options"

MANTI is a one-stop shop N-termini annotation & evaluation solution. MANTI was previously (un)known as muda.pl ahead of v3.7, the project was renamed to MANTI.pl with v3.7 on 2019-06-24. It congregates information from different MaxQuant or DiaNN/MSFragger output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred...

...All preprocessing actions are specified using common graphical elements organized into logically related blocks. The graphical user interface is implemented in Perl/Tk. In the command-line interface mode, all options need to be specified using the command line parameters. This way of non-interactive communication enables incorporating the application into a more complicated data mining process integrating several software packages or performing multiple conversions in a batch.

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

...It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to easily load and visualize the results using tools like UGENE (recommended) or artemis.

...When calculating the relative strength of each band (% of most prominent band) it takes the background noise into account. This leads to accurate and comparable results. Several options can be used to tune the detection process. Here we provide the source code of the program (Perl script) that can be run on any OS with Perl installed (e.g. the freely available Strawberry Perl). A Win-64bit executable is available at: www.foreach-bioinformatics.de

Gplot provides a convenient front-end for gnuplot. It accepts a large set of options to generate a single plot of one or more sets of data (overlaid as necessary).

latexdiff is a Perl script, which compares two latex files and marks up significant differences between them (i.e. a diff for latex files). Various options are available for visual markup using standard latex packages such as "color.sty".

Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25

Based on the Buckwalter Morphological Analyzer (Version 1.0) for doing Arabic stemming and POS tagging. Includes a rewrite of the original Perl script, with better documentation and more flexible options, and a C++ interface (usable as a library or app).