@@ -28,14 +28,15 @@ Rapid Peptides Generator (RPG) is dedicated to predict cleavage sites of proteas
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@@ -28,14 +28,15 @@ Rapid Peptides Generator (RPG) is dedicated to predict cleavage sites of proteas
Overview
Overview
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Rapid Peptides Generator (RPG), is dedicated to predict cleavage sites of proteases.
Rapid Peptides Generator (RPG), is a standalone software dedicated to predict proteases-induced cleavage sites on sequences.
RPG is a standalone python tools taking (multi-)fasta/fastq file of proteins as input and digest each of them. Digestion mode can be either concurrent, where all enzymes are present at the same time during digestion, or sequential. In sequential mode, each protein will be digested by each enzymes, one by one.
RPG is a python tool taking (multi-)fasta/fastq file of proteins as input and digest each of them. Digestion mode can be either 'concurrent', i.e. all enzymes are present at the same time during digestion, or 'sequential'. In sequential mode, each protein will be digested by each enzyme, one by one.
Resulting peptides contains informations about positions of cleavage site, peptide sequences, length, mass as-well as an estimation of isoelectric point (pI) of each peptide. Isoelectric point is the pH at which a peptide carries no net electrical charge and a good approximation can be computed on small molecules. Results are output in multi-fasta, CSV or TSV file.
The resulting peptides contain informations about positions of cleavage site, peptide sequences, length, mass as-well as an estimation of isoelectric point (pI) of each peptide. Shortly, the isoelectric point is the pH at which a peptide carries no net electrical charge and a good approximation can be computed on small molecules. Results are outputted in multi-fasta, CSV or TSV file.
Currently, there is 27 enzymes and chemicals in RPG. User can easily design new enzymes, using a simple yet powerful grammar. This grammar allows user to design complex enzymes like trypsin or thrombin, including many exceptions and different cleaving site. User-defined enzymes are then interpreted by RPG and user can use them as the regular one already available in the software.
Currently, 42 enzymes and chemicals are included in RPG. User can easily design new enzymes, using a simple yet powerful grammar. This grammar allows the user to design complex enzymes like trypsin or thrombin, including many exceptions and different cleavage sites. User-defined enzymes are then interpreted by RPG and included in the local installation of the software.
RPG follows the standards for software development with continuous integration on Gitlab (https://gitlab.pasteur.fr/nmaillet/rpg) and automatic on-line documentation (https://rapid-peptide-generator.readthedocs.io).
Installation
Installation
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@@ -48,7 +49,6 @@ In order to install RPG, you can use **pip**::
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@@ -48,7 +49,6 @@ In order to install RPG, you can use **pip**::
This command installs RPG and its Python dependencies.
This command installs RPG and its Python dependencies.
