SynBlast: assisting the analysis of conserved synteny information.

BMC Bioinformatics
Jörg LehmannSonja J Prohaska

Abstract

In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information. Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples. The SynBlast package written in Perl is available under the GNU General ...Continue Reading

References

Jan 24, 1992·Cell·W McGinnis, R Krumlauf
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 1, 1997·Molecular Biology and Evolution·W J BaileyF H Ruddle
Dec 22, 1999·Seminars in Cell & Developmental Biology·E J Stellwag
Jul 21, 2000·Radiographics : a Review Publication of the Radiological Society of North America, Inc·J C Honeyman, W W Olmsted
Mar 17, 2001·Nature Reviews. Genetics·D E Ferrier, P W Holland
Aug 29, 2001·Journal of Anatomy·P W Holland
Dec 18, 2001·Journal of Molecular Biology·M RemmE L Sonnhammer
Apr 5, 2002·Genome Research·W James Kent
Jan 17, 2003·Genome Research·Pavel Pevzner, Glenn Tesler
Mar 6, 2003·Genome Research·John S TaylorYves Van de Peer
Jan 7, 2004·Genome Research·Angel AmoresJohn H Postlethwait
Mar 23, 2004·Journal of Chemical Information and Computer Sciences·Claudia FriedPeter F Stadler
May 22, 2004·Nature Reviews. Genetics·Dario BoffelliEdward M Rubin
Jul 13, 2004·Bioinformatics·Brian J HaasSteven L Salzberg
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Manolis KellisEric S Lander
Dec 21, 2004·Nucleic Acids Research·Kevin P O'BrienErik L L Sonnhammer
Jun 22, 2005·Trends in Genetics : TIG·Simone Hoegg, Axel Meyer
Jun 24, 2005·Genetics·Wataru KaiYuzuru Suzuki
Sep 16, 2005·Molecular Biology and Evolution·Karen D CrowGünter P Wagner
Dec 13, 2005·Nature Reviews. Genetics·Jordi Garcia-Fernàndez
Apr 19, 2006·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Sonja J Prohaska, Peter F Stadler
Jun 1, 2006·Nature Genetics·Joost M Woltering, Antony J Durston
Jun 28, 2006·Proceedings of the National Academy of Sciences of the United States of America·John F MulleyPeter W H Holland
Jul 29, 2006·Bioinformatics·Andrey AlexeyenkoErik L L Sonnhammer
Sep 5, 2006·Genome Research·Carol SoderlundAndrew Paterson
Sep 20, 2006·Genome Research·Jian MaWebb Miller
Oct 3, 2006·PLoS Computational Biology·Leo Goodstadt, Chris P Ponting
Jun 8, 2007·Development·Denis Duboule
Oct 20, 2007·Nucleic Acids Research·Evgenia V KriventsevaEvgeny M Zdobnov
Nov 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Chunfang ZhengDavid Sankoff
Nov 15, 2007·Nucleic Acids Research·P FlicekS Searle
Dec 7, 2007·Nucleic Acids Research·Ann-Charlotte BerglundErik L L Sonnhammer
Jan 19, 2008·Theory in Biosciences = Theorie in Den Biowissenschaften·Sonja J Prohaska, Peter F Stadler

❮ Previous
Next ❯

Citations

Jun 28, 2011·Briefings in Bioinformatics·Colin N Dewey
Feb 16, 2013·Molecular Biology and Evolution·Marnix H MedemaRainer Breitling
Feb 26, 2014·BMC Bioinformatics·Raja Hashim AliLars Arvestad
Sep 2, 2009·Briefings in Bioinformatics·Jerome SalseCatherine Feuillet
Aug 20, 2014·PloS One·Marcus LechnerPeter F Stadler

❮ Previous
Next ❯

Software Mentioned

Ensembl
Compara
OrthoDB
getEnsemblProteins
Celera
Parahox
Ensembl Core
blastall
WU
Perl

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.