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BioPerl specifications

Information


Unique identifier OMICS_04849
Name BioPerl
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/BioPerl

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Documentation


Publications for BioPerl

BioPerl citations

 (429)
call_split

Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole Genome Phylogenetic Analysis

2018
PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17
call_split See protocol

[…] or isolates that did not have PCR results and to confirm previous conventional typing, WGS data were used: reads were assembled using SPAdes Genome Assembler (), and an in silico PCR script using the BioPerl () toolkit was used to search for SCCmec typing PCR primer sequences () and analyze in silico amplicons. For 10 isolates for which conventional typing and WGS typing results were discordant, r […]

library_books

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

2018
PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] onsynonymous (KA) substitution between pairs of collinear genes were estimated by aligning proteins with Clustal Omega [] and back-translating to nucleotides before calculating KA and KS values using BioPerl []. The collinearity of each block was calculated by dividing the number of collinear genes in a block by the total number of genes in the same region []. We also counted the number of colline […]

library_books

HMMER Cut off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut off threshold

2018
PLoS One
PMCID: 5868777
PMID: 29579071
DOI: 10.1371/journal.pone.0193757

[…] The HMMERCTTER pipeline is written in MATLAB (The MathWorks Inc., Natick, MA, USA) and calls a number of PERL scripts that depend on Bioperl [] and software packages. HMMER3 []: hmmbuild is used with default settings, hmmsearch with the option–noali. MSAs are constructed by MAFFTv7 []: with the settings–anysymbol–auto. Dendroscope […]

call_split

Automated high throughput animal CO1 metabarcode classification

2018
Sci Rep
PMCID: 5844909
PMID: 29523803
DOI: 10.1038/s41598-018-22505-4
call_split See protocol

[…] Three sets of CO1 reference sequences were assembled: 1) Arthropoda, 2) Chordata, and 3) outgroup taxa as described below using Perl with BioPerl modules and the Ebot script,. The following search terms were used to query the NCBI taxonomy database: 1) “Arthropoda”[ORGN] AND “species”[RANK] [Aug. 10, 2016], 2) “Chordata”[ORGN] AND “spec […]

library_books

Whole genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi feralization

2018
GigaScience
PMCID: 5905515
PMID: 29668959
DOI: 10.1093/gigascience/giy019

[…] terozygosity log2(HP ratio) over a 30-kb sliding window with a step of 15 kb (Supplementary Table S10–S14). FST distances between population were calculated using the Bio::PopGen::PopStats package in BioPerl []. The pooled heterozygosity HP for population was calculated using the formula H = 2∑p∑q/(∑p+∑q)2, where ∑p represents the sum of the major allele frequencies of all SNP sites in the window […]

library_books

Hierarchical interactions between Fnr orthologs allows fine tuning of transcription in response to oxygen in Herbaspirillum seropedicae

2018
Nucleic Acids Res
PMCID: 5934665
PMID: 29529262
DOI: 10.1093/nar/gky142

[…] bowtie2 software (), which resulted in one SAM (.sam) file for each fastq file. All further operations for the ChIP-Seq analysis were carried out using a combination of Perl scripts dependent on the BioPerl toolkit () and R scripts essentially as described previously (). Statistical significance of ChIP-Seq enriched peaks was determined by comparing the level of enrichment between the total and i […]

Citations

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BioPerl institution(s)
University Program in Genetics, Duke University, Durham, NC, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, Canada; AlgoNomics, Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, CA, USA; Affymetrix, Inc., Emeryville, CA, USA; Open Bioinformatics Foundation, Somerville, MA, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science, Washington University, St. Louis, MO, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, CA, USA; Cogina, New York City, NY, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institute of Molecular and Cell Biology, Singapore
BioPerl funding source(s)
Supported by the Open Bioinformatics Foundation; the Compaq and Sun Microsystems; NIH Genetics training grant T32 GM07754–22; NIH grant 1 K22 HG00056; NHGRI Grant K22 HG-00064-01; NIH grants HG00739 and P41HG02223 and EMBL core funding.

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