Topic
Perl
About: Perl is a research topic. Over the lifetime, 1442 publications have been published within this topic receiving 69765 citations. The topic is also known as: Practical Extraction and Reporting Language & Perl/CGI.
Papers published on a yearly basis
Papers
TL;DR: Prokka is introduced, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer, and produces standards-compliant output files for further analysis or viewing in genome browsers.
Abstract: UNLABELLED: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. AVAILABILITY AND IMPLEMENTATION: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/.
16,016 citations
TL;DR: A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented, based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit.
Abstract: A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.
15,028 citations
TL;DR: PRINSEQ is presented for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets and can be used as a stand alone version or accessed online through a user-friendly web interface.
Abstract: Summary: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis.
Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/.
Contact:[email protected]; [email protected]
4,883 citations
TL;DR: ABINITv3.0 is described, in which freedom of sources, reliability, portability, and self-documentation are emphasised, in the development of a sophisticated plane-wave pseudopotential code.
3,177 citations
TL;DR: This work has implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs.
Abstract: Summary: We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C.
Availability: The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.
3,132 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2025 | 10 |
| 2024 | 37 |
| 2023 | 41 |
| 2022 | 67 |
| 2021 | 16 |
| 2020 | 25 |