Brief Funct Genomic Proteomic. 2005 Jul;4(2):178-85.

A tiered approach to comparative genomics.

Source

Department of Biology, University of Alabama, Birmingham, AL, 35294, USA.

Abstract

Comparative genomics has emerged as a valuable tool for locating genes, transcription factor motifs and other putative control regions. There are, however, issues that keep comparative genomics from being a straightforward process. These caveats fall into three categories: database, computational and biological. In this review paper, these caveats will be discussed and illustrated using related case studies. The National Center for Biotechnology Information and University of California Santa Cruz genome databases were used, and VISTA, LAGAN and zPicture were used as comparison tools. Based on these caveats, a tiered approach to carrying out comparative genomic studies is presented.

PMID:: 16102272; [PubMed - indexed for MEDLINE]

Free full text

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Save items

Related citations in PubMed

Ab initio identification of putative human transcription factor binding sites by comparative genomics. [BMC Bioinformatics. 2005]
Ab initio identification of putative human transcription factor binding sites by comparative genomics.
Corà D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M. BMC Bioinformatics. 2005 May 2; 6:110. Epub 2005 May 2.
NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae. [BMC Bioinformatics. 2005]
NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae.
Rambaldi D, Guffanti A, Morandi P, Cassata G. BMC Bioinformatics. 2005 Dec 1; 6 Suppl 4:S22. Epub 2005 Dec 1.
GRAST: a new way of genome reduction analysis using comparative genomics. [Bioinformatics. 2006]
GRAST: a new way of genome reduction analysis using comparative genomics.
Toft C, Fares MA. Bioinformatics. 2006 Jul 1; 22(13):1551-61. Epub 2006 Apr 6.
Review Current bioinformatics tools in genomic biomedical research (Review). [Int J Mol Med. 2006]
Review Current bioinformatics tools in genomic biomedical research (Review).
Teufel A, Krupp M, Weinmann A, Galle PR. Int J Mol Med. 2006 Jun; 17(6):967-73.
Review Annotation, comparison and databases for hundreds of bacterial genomes. [Res Microbiol. 2007]
Review Annotation, comparison and databases for hundreds of bacterial genomes.
Médigue C, Moszer I. Res Microbiol. 2007 Dec; 158(10):724-36. Epub 2007 Oct 6.

See reviews... See all...

Cited by 2 PubMed Central articles

Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective. [PLoS One. 2011]
Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective.
de Groot GA, During HJ, Maas JW, Schneider H, Vogel JC, Erkens RH. PLoS One. 2011 Jan 26; 6(1):e16371. Epub 2011 Jan 26.
RNA interference in Schistosoma mansoni schistosomula: selectivity, sensitivity and operation for larger-scale screening. [PLoS Negl Trop Dis. 2010]
RNA interference in Schistosoma mansoni schistosomula: selectivity, sensitivity and operation for larger-scale screening.
Stefanić S, Dvořák J, Horn M, Braschi S, Sojka D, Ruelas DS, Suzuki B, Lim KC, Hopkins SD, McKerrow JH, et al. PLoS Negl Trop Dis. 2010 Oct 19; 4(10):e850. Epub 2010 Oct 19.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

A tiered approach to comparative genomics.
A tiered approach to comparative genomics.
Brief Funct Genomic Proteomic. 2005 Jul ;4(2):178-85.

PubMed
Implementation of a health care policy: an analysis of barriers and facilitators...
Implementation of a health care policy: an analysis of barriers and facilitators to practice change.
BMC Health Serv Res. 2005 Aug 15 ;5:53.

PubMed
Disruption of reproductive development in male rat offspring following in utero ...
Disruption of reproductive development in male rat offspring following in utero exposure to phthalate esters.
Int J Androl. 2006 Feb ;29(1):140-7; discussion 181-5. Epub 2005 Aug 11 .

PubMed
Rhamnolipids mediate detachment of Pseudomonas aeruginosa from biofilms.
Rhamnolipids mediate detachment of Pseudomonas aeruginosa from biofilms.
Mol Microbiol. 2005 Sep ;57(5):1210-23.

PubMed
Aspirin downregulates homocysteine formation in stimulated human peripheral bloo...
Aspirin downregulates homocysteine formation in stimulated human peripheral blood mononuclear cells.
Scand J Immunol. 2005 Aug ;62(2):155-60.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to:

A tiered approach to comparative genomics.

Source

Abstract

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Cited by 2 PubMed Central articles

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information