npsearch 2.0.0 → 2.0.1
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- data/README.md +104 -53
- data/lib/npsearch/version.rb +1 -1
- data/npsearch.gemspec +2 -1
- metadata +5 -4
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data/README.md
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#
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[](http://inch-ci.org/github/IsmailM/NeuroPeptideSearch)
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# NpSearch (NeuroPeptideSearch)
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[](https://travis-ci.org/wurmlab/NpSearch)
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[](http://badge.fury.io/rb/npsearch)
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[](https://gemnasium.com/wurmlab/NpSearch)
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> A tool to identify noval Neuropeptides.
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NpSearch (NeuroPeptideSearch) is a program that searches for potential neuropeptides precursors based on the motifs commonly found on a neuropeptide. Ideally, the input would be transcriptome or protein data since there are no introns to worry about and the signal peptide would be attached to the front of the precursor.
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## Introduction
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NpSearch is a tool that helps identify novel neuropeptides. As such it is not based on homology to existing neuropeptides - rather NpSearch is based on the common characteristics of neuropeptides and their precursors.
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If you use this program, please cite us:
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>Moghul I, Rowe M, Priyam A, ELphick M & Wurm Y <em>(in prep)</em> NpSearch: A Tool to Identify Novel Neuropeptides
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NpSearch produces a fasta file and highly visual html file that are ordered by the likelihood of a sequence encoding a neuropeptide precursor.
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NpSearch orders the results based on the following characteristics:
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- **Signal peptide**: All neuropeptide precursors must have a signal peptide. This is due to the fact that the final bioactive neuropeptide has to be secreted from the cell of synthesis in order to be functionally active.
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- **Cleavage sites**: Being derived from a precursor, the bioactive neuropeptide has to be cleaved out from the precursor. Prohormone convertase enzymes cleave these bioactive peptides at specific cleavage sites. Since certain cleavage motifs are more likely to be cleaved, NpSearch awards sequences with cleavage site motifs that are more likely to be cleaved with a higher score.
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- **C-terminal Glycine**: A significant number of bioactive neuropeptides have a C-terminal glycine, that is amidated during post-translation modification. NpSearch awards sequences that have a potential neuropeptide with a C-terminal glycine a higher score.
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- **Repeated peptides**: Some neuropeptide precursors contain numerous copies of the same neuropeptides (usually with slight sequence differences). NpSearch attempts to detect this by aligning all potential neuropeptides within a sequence. If a sequence is found to have multiple, similar predicted NPs, NpSearch awards it with a higher score.
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- **Acidic spacer regions**: Neuropeptide precursors that contain multiple neuropeptide copies tend to have highly acidic spacer regions that separate the NP copies. If detected by NpSearch, the sequence is awarded with a higher score.
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## Installation
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### Installation Requirements
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* Ruby (>= 2.0.0)
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* SignalP 4.1 (Available from [here](http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp))
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* USearch (Available from [here]())
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* A web browser.
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## Installation
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Simply run the following command in the terminal.
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```bash
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gem install npsearch
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```
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If that doesn't work, try `sudo gem install npsearch` instead.
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##### Running From Source (Not Recommended)
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It is also possible to run from source. However, this is not recommended.
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```bash
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# Clone the repository.
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git clone https://github.com/wurmlab/npsearch.git
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# Move into NpSearch source directory.
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cd NpSearch
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# Install bundler
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gem install bundler
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# Use bundler to install dependencies
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bundle install
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# Optional: run tests, build documentation and build the gem from source
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bundle exec rake
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# Run NpSearch.
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bundle exec npsearch -h
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# note that `bundle exec` executes NpSearch in the context of the bundle
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# Alternativaly, install NpSearch as a gem
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bundle exec rake install
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npsearch -h
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```
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## Usage
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Verify NpSearch installed by running the following command in the terminal:
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```bash
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npsearch
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```
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You should see the following output.
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```bash
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* Usage: npsearch [Options] -i [Input File]
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* Mandatory Options:
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-i, --input [file] Path to the input fasta file
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* Optional Options:
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-s, --signalp_path The full path to the signalp script. This can be downloaded from
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CBS. See https://www.github.com/wurmlab/NpSearch for more
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information
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-u, --usearch_path The full path to the usearch binary. This script can be downloaded
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from .... See https://www.github.com/wurmlab/NpSearch for more
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information
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-n, --num_threads The number of threads to use when analysing the input file
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-m, --orf_min_length N The minimum length of a potential neuropeptide precursor.
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Default: 30
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-h, --help Display this screen
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-v, --version Shows version
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```
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### Example Usage Scenario
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The following runs NpSearch on an input fasta dataset.
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```bash
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npsearch -i INPUT_FASTA_FILE -s /path/to/signalp -u /path/to/usearch -n NUM_THREADS
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```
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## Output
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The output produced by NpSearch is presented in two manners. NpSearch produces a highly visual HTML file that can be open in any browsers (an example can seen [here]()) and a fasta file.
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* Usage: npsearch [Options] -i [Input File] -o [Output Folder Name]
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* Mandatory Options:
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-i, --input [file] The input file (in fasta format). Can be a relative or a full
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path.
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-o, --output [folder name] The path to the output folder. This will be created if the
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folder does not exist.
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* Optional Options:
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-m, --motif [Query Motif] By default NpSearch only searches for dibasic cleavage site
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("KR", "RR" or "KK"). This option allows one to change the
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set of cleavage sites to be searched.
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The period "." can be used to denote any character. Multiple
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motifs query can be used by using a pipeline character ("|")
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between each query and putting the motif query in speech marks
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e.g. "KR|RR|R..R"
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Advanced Users: Regular expressions are supported.
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-c, --cut_off N Changes the minimum Open Reading
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Frame from the default 10 amino acid residues to N amino acid
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residues.
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-s, --signalp_file [file] Is used to supply the signal peptide results to the program.
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These signal peptide results must be created using the SignalP
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program (Version 4.x), downloadable from CBS. If this argument
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isn't suplied, then NpSearch will try to run a local version
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of the Signal P script.
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-e, --extract_orf Only extracts the Open Reading Frames.
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-v, --verbose Provides more information on each step taken in this program.
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-h, --help Display this screen
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--version Shows version
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/lib/npsearch/version.rb
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data/npsearch.gemspec
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s.description = 'Search for Neuropeptides based solely on the common' \
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' neuropeptide markers (e.g. signal peptide, dibasic' \
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' cleavage sites etc.) i.e. not based on homology to' \
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" known neuropeptides.\n\n" \
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' For more information: https://github.com/wurmlab/npsearch'
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s.summary = 'Search for neuropeptides based on the common' \
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' neuropeptides markers'
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s.homepage = 'https://github.com/IsmailM/NeuroPeptideSearch'
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metadata
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--- !ruby/object:Gem::Specification
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name: npsearch
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version: !ruby/object:Gem::Version
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version: 2.0.
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version: 2.0.1
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platform: ruby
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authors:
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- Ismail Moghul
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.0'
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description:
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(e.g. signal peptide, dibasic cleavage sites etc.) i.e. not based on homology to
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description: |-
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Search for Neuropeptides based solely on the common neuropeptide markers (e.g. signal peptide, dibasic cleavage sites etc.) i.e. not based on homology to known neuropeptides.
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For more information: https://github.com/wurmlab/npsearch
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email:
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- y.wurm@qmul.ac.uk
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executables:
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