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Protocols

PipMaker specifications

Information


Unique identifier OMICS_00944
Name PipMaker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two genomic sequences.
Input format FASTA
Output data A percent identity plot.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • Laj
  • MultiPipTools
  • Tffind

Versioning


No version available

Maintainer


  • person_outline PipMaker Team

Additional information


http://pipmaker.bx.psu.edu/pipmaker/

Information


Unique identifier OMICS_00944
Name PipMaker
Interface Web user interface
Restrictions to use None
Input data Two genomic sequences.
Input format FASTA
Output data A percent identity plot.
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • Laj
  • MultiPipTools
  • Tffind

Maintainer


  • person_outline PipMaker Team

Additional information


http://pipmaker.bx.psu.edu/pipmaker/

Publications for PipMaker

PipMaker citations

 (131)
call_split

Identification of novel cis regulatory elements of Eya1 in Xenopus laevis using BAC recombineering

2017
Sci Rep
PMCID: 5670250
PMID: 29101371
DOI: 10.1038/s41598-017-15153-7
call_split See protocol

[…] s was used as a reference genome and was compared with human, mouse, rat and chick genomes using ECR browser (http://ecrbrowser.dcode.org), VISTA browser (http://genome.lbl.gov/vista/index.shtml) and Pipmaker (http://pipmaker.bx.psu.edu/pipmaker/). […]

library_books

Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci

2017
Immunogenetics
PMCID: 5871656
PMID: 28924718
DOI: 10.1007/s00251-017-1028-0

[…] Sequences were masked using RepeatMasker and alignment plots generated using PipMaker (; Schwartz ). […]

library_books

Evolution of the vertebrate insulin receptor substrate (Irs) gene family

2017
BMC Evol Biol
PMCID: 5482937
PMID: 28645244
DOI: 10.1186/s12862-017-0994-z

[…] ciprocal BLASTx searches of the mouse proteomes to ensure that their best matches were Irs-like sequences.To examine genomic neighborhoods near Irs-like genes genomic comparisons were conducted using PipMaker and MultiPipMaker [, ]. Genes neighboring the Irs-like genes were identified from the genome assemblies in Ensembl [] and the Elephant Shark Genome Project []. The organization of genes adjac […]

call_split

Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters

2017
Genome Announc
PMCID: 5481585
PMID: 28642379
DOI: 10.1128/genomeA.00572-17
call_split See protocol

[…] lel with MHAP, as implemented in Canu version 1.0 (), using the complete set of subreads from the single-molecule real-time (SMRT) cell. The two assemblies were compared by generating a dot plot with PipMaker () and found to match. To circularize the genome, overlapping ends in the longer Canu assembly were trimmed with Artemis version 16.0.0 (). Base calling was then corrected with the RS_Reseque […]

library_books

Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing1

2017
Appl Plant Sci
PMCID: 5435405
PMID: 28529832
DOI: 10.3732/apps.1700002

[…] value of 1e-10. The reference species for annotation was Cryptomeria japonica (GenBank accession no. AP009377). The annotated chloroplast genome was visualized as a circular genome using GenomeVx (). PipMaker () was used to create dot plots and gene identity plots between C. sulcata and another Cupressaceae species, Calocedrus formosana (Florin) Florin (GenBank accession no. AB831010).We used MSAT […]

library_books

Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long read sequencing technology

2017
Sci Rep
PMCID: 5374520
PMID: 28361880
DOI: 10.1038/srep45518

[…] of matched base pairs in the alignment to the total number of events, where each base pair substitution and each INDEL was regarded as a single event, independent of size. We analysed variation with PipMaker dot-plot and Mauve version snapshot_2015-2-25. Genomic sequence of the small structural discrepancies was compared to the genomic repetitive elements in Repbase Update database. […]

Citations

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PipMaker institution(s)
The Pennsylvania State University, University Park, PA, USA
PipMaker funding source(s)
Supported by grant HG02238 from the National Human Genome Research Institute.

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