Direct mapping and alignment of protein sequences onto genomic sequence

Bioinformatics
Osamu Gotoh

Abstract

Finding protein-coding genes in a newly determined genomic sequence is the first step toward understanding the content written in the genome. Sequences of transcripts of homologous genes, if available, can considerably improve accuracy of prediction of genes and their structures, compared with that without such knowledge. As protein sequences are generally better conserved than nucleotide sequences, remote homologs can be used as templates, extending the applicability of evidence-based gene recognition methods. However, no tool seems to have been developed so far to simultaneously map and align a number of protein sequences on mammalian-sized genomic sequence. We have extended our computer program Spaln to accept protein sequences, as well as cDNA sequences, as queries. When the query and the target sequences are reasonably similar, e.g. between mammalian orthologs, Spaln runs one to two orders of magnitude faster than conventional approaches that rely on Blast search followed by dynamic-programming-based spliced alignment. Exon-level and gene-level accuracies of Spaln are significantly higher than those obtained by the best available methods of the same type, particularly when the query and the target are distantly related. Sp...Continue Reading

References

Jun 1, 1992·Computer Applications in the Biosciences : CABIOS·D T JonesJ M Thornton
Jan 1, 1988·Bulletin of Mathematical Biology·W Miller, E W Myers
Jan 10, 1986·Nucleic Acids Research·H PeltolaE Ukkonen
Sep 11, 1995·Nucleic Acids Research·M BorodovskyA Danchin
Mar 21, 1994·Journal of Theoretical Biology·J Hein
Oct 1, 1993·Computer Applications in the Biosciences : CABIOS·M Q Zhang, T G Marr
Jun 15, 1996·Genomics·M Burset, R Guigó
Aug 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·M S GelfandP A Pevzner
Dec 1, 1996·Computer Applications in the Biosciences : CABIOS·X Huang, J Zhang
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 1, 1997·Computer Applications in the Biosciences : CABIOS·S L Salzberg
Dec 24, 1997·Genomics·W R PearsonW Miller
Dec 24, 1997·Genomics·X HuangA R Kerlavage
Dec 16, 1998·Science·UNKNOWN C. elegans Sequencing Consortium
Oct 24, 2000·Genome Research·R GuigóJ W Fickett
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
May 5, 2001·Genome Research·S RogicF B Ouellette
Apr 5, 2002·Genome Research·W James Kent
Apr 6, 2002·Bioinformatics·Bin MaMing Li
Oct 3, 2003·Current Biology : CB·Olga Zhaxybayeva, J Peter Gogarten
Nov 25, 2003·Journal of Molecular Evolution·Ming OuyangJoan Burnside
Feb 7, 2004·Nucleic Acids Research·Irmtraud M Meyer, Richard Durbin
May 5, 2004·Genome Research·Val CurwenMichele Clamp
May 5, 2004·Genome Research·Ewan BirneyRichard Durbin
Jun 25, 2004·Nucleic Acids Research·Mario StankeBurkhard Morgenstern
Jul 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Avril Coghlan, Kenneth H Wolfe
Oct 22, 2004·Nature·UNKNOWN International Human Genome Sequencing Consortium
Nov 25, 2004·PLoS Biology·Cydney B NielsenJames E Galagan
Feb 17, 2005·BMC Bioinformatics·Guy St C Slater, Ewan Birney
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Jun 18, 2005·Bioinformatics·Brona BrejováTomás Vinar
Aug 4, 2005·Bioinformatics·Jonathan E Allen, Steven L Salzberg
Dec 24, 2005·Nature·Masayuki MachidaHisashi Kikuchi
Dec 31, 2005·Nucleic Acids Research·David L WheelerEugene Yaschenko
Apr 8, 2006·Genome Biology·Sourav Chatterji, Lior Pachter
May 10, 2006·PLoS Genetics·Erik van NimwegenMihaela Zavolan
Jul 18, 2006·Nucleic Acids Research·Shu Ju HsiehChuan Yi Tang
Oct 19, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Daniel G Brown
May 15, 2007·Genome Research·Liran CarmelEugene V Koonin
Jul 25, 2007·Bioinformatics·Xuefeng CuiMing Li
Aug 11, 2007·Genome Research·David DeCaprioJames E Galagan

❮ Previous
Next ❯

Citations

Mar 10, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Kai SongFang Wu
May 4, 2010·BMC Bioinformatics·Ryuichiro Nakato, Osamu Gotoh
Jun 13, 2012·Biological & Pharmaceutical Bulletin·Osamu Gotoh
Mar 10, 2018·Nature Communications·Vicencio OostraChristopher W Wheat
Apr 7, 2019·GigaScience·Wenbo ChenGeorg Jander
Oct 17, 2017·Journal of Biochemistry·Chisato NoguchiYuri Aoyama
May 23, 2020·NAR Genomics and Bioinformatics·Tomáš BrůnaMark Borodovsky
Feb 13, 2021·NAR Genomics and Bioinformatics·Tomáš BrůnaMark Borodovsky

❮ Previous
Next ❯

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.