Pecan protocols

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Pecan specifications

Information


Unique identifier OMICS_03739
Name Pecan
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output data A file containing a formatted alignment.
Output format FASTA
Operating system Unix/Linux
Programming languages Java, Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
Exonerate
Maintained No

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Publications for Pecan

Pecan in pipelines

 (2)
2013
PMCID: 3764194
PMID: 24039605
DOI: 10.1371/journal.pgen.1003763

[…] probes shared between human and chimpanzee., to investigate the global correspondence of dna sequence differences between species and the degree of methylation changes, we examined the enredo-pecan-orthus (epo) whole-genome multiple alignments of human, chimpanzee, gorilla, and orangutan [ensemble compara.6_primates_epo] , . considering only those blocks with alignments for all great […]

2009
PMCID: 2808936
PMID: 19906699
DOI: 10.1093/nar/gkp972

[…] all of the low coverage mammalian genome sequences and now provide bed files for human and mouse constrained elements as determined by alignments of placental mammals. the recently published enredo-pecan-ortheus (epo) pipeline is at the heart of ensembl’s msa computations (,,)., ensembl genetrees are the result of a comprehensive analysis to predict phylogeny in vertebrates and have recently […]


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Pecan in publications

 (28)
PMCID: 5891062
PMID: 29590096
DOI: 10.1371/journal.pgen.1007254

[…] (ii) the ucsc multiz (mz) 46-way alignments [] downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/multiz46way/ and (iii) ensembl enredo, pecan, ortheus (epo) 6 primate multiple alignment, release 74, [] downloaded from ftp://ftp.ensembl.org/pub/release-74/emf/ensembl-compara/epo_6_primate/. we found that the epo alignments […]

PMCID: 5543444
PMID: 28774272
DOI: 10.1186/s12864-017-3964-3

[…] from whole genome alignments of 6 primate species (h. sapiens, p. troglodytes, g. gorilla, p. pygmaeus, m. mulatta and c. jacchus) released in ensembl compara 59 which implemented the enredo-pecan-ortheus (epo) alignment method []. we accessed this information from phase 1 of the 1000 genomes project [] by applying the tabix command from the sam tools package [] to the relevant […]

PMCID: 4845318
PMID: 27113450
DOI: 10.1186/s12864-016-2622-5

[…] overlap with previous cut annotations, we included all antisense, same sense, and intergenic (i.e. a, b, and i) clusters with an rrp6δ/wt fold change ≥ 1.5 as calculated in their study., we used pecan version 0.9 [, ] to generate a four-way whole genome multiple sequence alignment of the s288c, σ1278b, jay291, and n17 genomes. as the jay291 genome is currently only available in a contig […]

PMCID: 4761110
PMID: 26896847
DOI: 10.1093/database/bav096

[…] of pairs of species. it is also worth noting that these syntenic blocks are not intended to show duplications in one species with respect to another. duplications are presented in the enredo-pecan-ortheus (epo) whole-genome alignments (, ) which specifically support such features and are described below., our multiple alignments are built with pecan (), which uses a consistency-based […]

PMCID: 4608704
PMID: 26474060
DOI: 10.1371/journal.pgen.1005579

[…] populations (asw, ceu, chb, chs, clm, fin, gbr, ibs, jpt, lwk, mxl, pur, tsi and yri)., orthologs of human retrocopies in 13 other eutherian species were identified using amniota vertebrates pecan [] whole genome alignment from ensembl release 73 [], requiring a reciprocal overlap of at least 50% between retrocopy sequences from different organisms in the alignment. to be more specific, […]


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Pecan institution(s)
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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