Literature DB >> 18287711

An Introduction to BioPerl.

Jason E Stajich1.   

Abstract

The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record.

Mesh:

Year:  2007        PMID: 18287711     DOI: 10.1007/978-1-59745-535-0_26

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  17 in total

1.  Evolutionary rate covariation reveals shared functionality and coexpression of genes.

Authors:  Nathan L Clark; Eric Alani; Charles F Aquadro
Journal:  Genome Res       Date:  2012-01-27       Impact factor: 9.043

2.  Scientific workflow management in proteomics.

Authors:  Jeroen S de Bruin; André M Deelder; Magnus Palmblad
Journal:  Mol Cell Proteomics       Date:  2012-03-12       Impact factor: 5.911

3.  SmedGD 2.0: The Schmidtea mediterranea genome database.

Authors:  Sofia M C Robb; Kirsten Gotting; Eric Ross; Alejandro Sánchez Alvarado
Journal:  Genesis       Date:  2015-07-17       Impact factor: 2.487

4.  Mining new crystal protein genes from Bacillus thuringiensis on the basis of mixed plasmid-enriched genome sequencing and a computational pipeline.

Authors:  Weixing Ye; Lei Zhu; Yingying Liu; Neil Crickmore; Donghai Peng; Lifang Ruan; Ming Sun
Journal:  Appl Environ Microbiol       Date:  2012-04-27       Impact factor: 4.792

5.  A quick guide for developing effective bioinformatics programming skills.

Authors:  Joel T Dudley; Atul J Butte
Journal:  PLoS Comput Biol       Date:  2009-12-24       Impact factor: 4.475

6.  Hypermethylation of OPRM1 promoter region in European Americans with alcohol dependence.

Authors:  Huiping Zhang; Aryeh I Herman; Henry R Kranzler; Raymond F Anton; Arthur A Simen; Joel Gelernter
Journal:  J Hum Genet       Date:  2012-08-23       Impact factor: 3.172

7.  Computational large-scale mapping of protein-protein interactions using structural complexes.

Authors:  Benjamin Shoemaker; Stefan Wuchty; Anna R Panchenko
Journal:  Curr Protoc Protein Sci       Date:  2013-09-24

8.  RF-Cloning.org: an online tool for the design of restriction-free cloning projects.

Authors:  Stephen R Bond; Christian C Naus
Journal:  Nucleic Acids Res       Date:  2012-05-08       Impact factor: 16.971

9.  Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes.

Authors:  Regina Z Cer; Kevin H Bruce; Uma S Mudunuri; Ming Yi; Natalia Volfovsky; Brian T Luke; Albino Bacolla; Jack R Collins; Robert M Stephens
Journal:  Nucleic Acids Res       Date:  2010-11-21       Impact factor: 16.971

10.  A "candidate-interactome" aggregate analysis of genome-wide association data in multiple sclerosis.

Authors:  Rosella Mechelli; Renato Umeton; Claudia Policano; Viviana Annibali; Giulia Coarelli; Vito A G Ricigliano; Danila Vittori; Arianna Fornasiero; Maria Chiara Buscarinu; Silvia Romano; Marco Salvetti; Giovanni Ristori
Journal:  PLoS One       Date:  2013-05-16       Impact factor: 3.240

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