BioPerl protocols

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chevron_left Phylogenetic inference Multiple nucleotide sequence alignment Nucleotide sequence homology search Pairwise nucleotide sequence alignment File indexation Libraries/frameworks chevron_right
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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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Publications for BioPerl

BioPerl in pipelines

 (37)
2018
PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17

[…] 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, […]

2017
PMCID: 5292693
PMID: 28165059
DOI: 10.1038/srep42094

[…] sequenced on an illumina hiseq 2500 platform and 50 bp single-end reads were generated., clean reads and count number of three mrna transcriptome libraries were assessed and summarized using custom bioperl scripts. with bowtie2 software, all clean reads were mapped back onto clementina genome sequence (cclementina_182_v1.0) which was downloaded from phytozome database […]

2017
PMCID: 5578505
PMID: 28859126
DOI: 10.1371/journal.pone.0183925

[…] as a pcr target were excluded immediately. see the diagram in for a schematic overview of the approach. the analysis included complete genomes and genome sequences in contigs. the script requires bioperl and was run using perl v5.18.2. the script is available on github (https://github.com/koenverst/slidingframe/)., overlapping frames that were conserved in s. pseudintermedius genomes […]

2017
PMCID: 5700742
PMID: 29166879
DOI: 10.1186/s12864-017-4306-1

[…] that consisted of at least 90% gaps were removed; this was done using trimal v1.2 []. after this, the tf family being analyzed had sequences with 95% similarity or more removed using a custom bioperl script that we designed, and was re-aligned. this cycle was repeated until the number of sequences and number of alignment columns stabilized., phylogenetic trees were generated using raxml […]

2016
PMCID: 4775055
PMID: 26934712
DOI: 10.1371/journal.pone.0150599

[…] requiring an overlap of 100 bases with < 5% difference, using ea-utils (v.1.1.2–537; https://code.google.com/p/ea-utils/). high quality joined sequences were converted from fastq to fasta using bioperl (www.bioperl.org) and processed using mothur v.1.30.1 []. briefly, sequences with ambiguous bases were excluded, as were sequences that: (1) did not align to the v4 region of the silva 16s […]


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BioPerl in publications

 (506)
PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17

[…] 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, […]

PMCID: 5844909
PMID: 29523803
DOI: 10.1038/s41598-018-22505-4

[…] involves making this method available through a web portal., 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] […]

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

[…] 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 […]

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 […]

PMCID: 5836831
PMID: 29504899
DOI: 10.1186/s12864-018-4478-3

[…] confluence., we analyzed dna sequences between nucleotide positions -70 and -20 upstream of the protein-coding regions in the human genes retrieved from the human reference genome using the standard bioperl library [] via our web service [] in the case of ancestral alleles of snps under study, as described in fig. . in the case of minor alleles of these snps, we created sequences by hand using […]


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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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