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The computational challenges of applying comparative-based computational methods to whole genomes

Dubchak, Inna and Pachter, Lior (2002) The computational challenges of applying comparative-based computational methods to whole genomes. Briefings in Bioinformatics, 3 (1). pp. 18-22. ISSN 1467-5463. doi:10.1093/bib/3.1.18. https://resolver.caltech.edu/CaltechAUTHORS:20170309-093904962

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Abstract

The explosion in genomic sequence avaliable in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tools will play a fundamental role in analysing the enormous amount of new data that is currently being generated. The synthesis of computationally intensive comparative computational approaches with the requirement for computational scientists. We focus on a few of these challenges, using by way of example the problems of alignment, gene and finding and regulatory element discovery, and discuss the issues that have arisen in attempts to solve these problems in the context of whole genome analysis pipelines.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/bib/3.1.18DOIArticle
https://academic.oup.com/bib/article/3/1/18/193661/The-computational-challenges-of-applyingPublisherArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2002 Henry Stewart Publications. We thank Dr Edward Rubin for helpful discussions. This work was supported by one of the 11 Programs for Genomic Applications (PGAs) funded by the National Heart, Lung, and Blood Institute (NHLBI).
Funders:
Funding AgencyGrant Number
National Heart, Lung, and Blood InstituteUNSPECIFIED
Subject Keywords:comparative genomics, whole genomes, sequence alignment, gene finding, regulatory elements
Issue or Number:1
DOI:10.1093/bib/3.1.18
Record Number:CaltechAUTHORS:20170309-093904962
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170309-093904962
Official Citation:Inna Dubchak, Lior Pachter; The computational challenges of applying comparative-based computational methods to whole genomes. Brief Bioinform 2002; 3 (1): 18-22. doi: 10.1093/bib/3.1.18
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74969
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:10 Mar 2017 23:12
Last Modified:15 Nov 2021 16:29

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