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Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
- Charles Y. Feigin,
- Axel H. Newton,
- and Andrew J. Pask
Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
...the thylacine data (Feigin et al. 2018). The average identity, calculated using BioPerl (Stajich et al. 2002), was high for both thylacine–Tasmanian devil and wolf–panda alignments (∼94.68% and 93.36%, respectively), indicating that TAR and WAR evolutionary rates are not driven by poor sequence quality. Given...
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Research: Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia
- Xiao Gou,
- Zhen Wang,
- Ning Li,
- Feng Qiu,
- Ze Xu,
- Dawei Yan,
- Shuli Yang,
- Jia Jia,
- Xiaoyan Kong,
- Zehui Wei,
- Shaoxiong Lu,
- Linsheng Lian,
- Changxin Wu,
- Xueyan Wang,
- Guozhi Li,
- Teng Ma,
- Qiang Jiang,
- Xue Zhao,
- Jiaqiang Yang,
- Baohong Liu,
- Dongkai Wei,
- Hong Li,
- Jianfa Yang,
- Yulin Yan,
- Guiying Zhao,
- Xinxing Dong,
- Mingli Li,
- Weidong Deng,
- Jing Leng,
- Chaochun Wei,
- Chuan Wang,
- Huaming Mao,
- Hao Zhang,
- Guohui Ding,
- and Yixue Li
Genome Res. August 2014 24: 1308-1315; Published in Advance April 10, 2014, doi:10.1101/gr.171876.113
...by distruct (v1.1) (Rosenberg 2004) on a per-individual basis. Standard population genetic statistics, includingWatterson’s u, pairwise nucleotide diversityp (Supplemental Fig. 2), andTajima’sD (Supplemental Fig. 3) were calculated for each breed by the Bio∷PopGen∷Statistics package in BioPerl (v1...
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Methods: Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis
- Shawn Hoon,
- Kiran Kumar Ratnapu,
- Jer-ming Chia,
- Balamurugan Kumarasamy,
- Xiao Juguang,
- Michele Clamp,
- Arne Stabenau,
- Simon Potter,
- Laura Clarke,
- and Elia Stupka
Genome Res. August 2003 13: 1904-1915; Published in Advance July 17, 2003, doi:10.1101/gr.1363103
...part of the programming work in bioinformatics involves writing “scripting glue,” for purposes that include connecting different software applications together, file format conversions, and information extraction. It is for this reason that software toolkits like Bioperl ( Stajich et al.2002 ) have...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
....6 (Junier and Zdobnov 2010) and calculated gsi statistics on the rooted treewith a custom-made Perl script using the BioPerl Tree module (Stajich et al. 2002). Species tree reconstruction To infer the species tree of the four closely related flycatcher species and the two outgroups, we analyzed a large...
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RESOURCE: EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- Albert J. Vilella,
- Jessica Severin,
- Abel Ureta-Vidal,
- Li Heng,
- Richard Durbin,
- and Ewan Birney
Genome Res. February 2009 19: 327-335; Published in Advance November 24, 2008, doi:10.1101/gr.073585.107
...toolkit: Perl modules for the life sciences . Genome Res. 12 : 1611 – 1618 . ↵ Wheeler, D.L. , Barrett, T. , Benson, D.A. , Bryant, S.H. , Canese, K. , Chetvernin, V. , Church, D.M. , Dicuccio, M. , Edgar, R. , Federhen, S. , et al. ( 2008 ) Database resources of the National Center for Biotechnology...
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Research: PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX
- Erwan Delbarre,
- Kristina Ivanauskiene,
- Jane Spirkoski,
- Akshay Shah,
- Kristin Vekterud,
- Jan Øivind Moskaug,
- Stig Ove Bøe,
- Lee H. Wong,
- Thomas Küntziger,
- and Philippe Collas
Genome Res. June 2017 27: 913-921; Published in Advance March 24, 2017, doi:10.1101/gr.215830.116
..., Lapp H, et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611–1618. Torok D, Ching RW, Bazett-Jones DP. 2009. PML nuclear bodies as sites of epigenetic regulation. Front Biosci 14: 1325–1336. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ...
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Method: Detection of structural mosaicism from targeted and whole-genome sequencing data
- Daniel A. King,
- Alejandro Sifrim,
- Tomas W. Fitzgerald,
- Raheleh Rahbari,
- Emma Hobson,
- Tessa Homfray,
- Sahar Mansour,
- Sarju G. Mehta,
- Mohammed Shehla,
- Susan E. Tomkins,
- Pradeep C. Vasudevan,
- Matthew E. Hurles,
- and The Deciphering Developmental Disorders Study
Genome Res. October 2017 27: 1704-1714; Published in Advance August 30, 2017, doi:10.1101/gr.212373.116
...were calculated as described in the following two paragraphs. Bdev values were generated using the following method: the identity of the alleles at each locus is extracted using fast_pileup function in the Perl module Bio::DB::Sam (Stajich et al. 2002), using high-quality reads (removal criteria: below...
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ENSEMBL Special: The Ensembl Core Software Libraries
- Arne Stabenau,
- Graham McVicker,
- Craig Melsopp,
- Glenn Proctor,
- Michele Clamp,
- and Ewan Birney
Genome Res. May 2004 14: 929-933; doi:10.1101/gr.1857204
...., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., et al. 2002 . The Bioperl Toolkit: Perl modules for the life sciences. Genome Res. 12 : 1611 -1618. ↵ Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., and Spieth, J. 2001 . WormBase: Network access to the and biology of Caenorhabditis elegans. Nucleic...
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Resource: JBrowse: A next-generation genome browser
- Mitchell E. Skinner,
- Andrew V. Uzilov,
- Lincoln D. Stein,
- Christopher J. Mungall,
- and Ian H. Holmes
Genome Res. September 2009 19: 1630-1638; Published in Advance July 1, 2009, doi:10.1101/gr.094607.109
...-annotation:Awiki solution?GenomeBiol8:102. Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C, Fuellen G, Gilbert J, Korf I, Lapp H. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611–1618. Stalker J, Gibbins B, Meid P, Smith J, Spooner W, Hotz H-R, Cox AV. 2004. The Ensembl...
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RESOURCE: The Generic Genome Browser: A Building Block for a Model Organism System Database
- Lincoln D. Stein,
- Christopher Mungall,
- ShengQiang Shu,
- Michael Caudy,
- Marco Mangone,
- Allen Day,
- Elizabeth Nickerson,
- Jason E. Stajich,
- Todd W. Harris,
- Adrian Arva,
- and Suzanna Lewis
Genome Res. October 1, 2002 12: 1599-1610; doi:10.1101/gr.403602
...that were not produced as part of this project are shown in a lighter color. BioPerl and Bio::Graphics Software Libraries Beneath gbrowse are two software libraries. The Bioperl library (Stajich et al., this issue) is responsible for interceding between the CGI script and the underlying database...

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