EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches

Genome Research
Biju Issac, Gajendra Pal Singh Raghava

Abstract

EGPred is a Web-based server that combines ab initio methods and similarity searches to predict genes, particularly exon regions, with high accuracy. The EGPred program proceeds in the following steps: (1) an initial BLASTX search of genomic sequence against the RefSeq database is used to identify protein hits with an E-value <1; (2) a second BLASTX search of genomic sequence against the hits from the previous run with relaxed parameters (E-values <10) helps to retrieve all probable coding exon regions; (3) a BLASTN search of genomic sequence against the intron database is then used to detect probable intron regions; (4) the probable intron and exon regions are compared to filter/remove wrong exons; (5) the NNSPLICE program is then used to reassign splicing signal site positions in the remaining probable coding exons; and (6) finally ab initio predictions are combined with exons derived from the fifth step based on the relative strength of start/stop and splice signal sites as obtained from ab initio and similarity search. The combination method increases the exon level performance of five different ab initio programs by 4%-10% when evaluated on the HMR195 data set. Similar improvement is observed when ab initio programs are ev...Continue Reading

References

Mar 1, 1993·Nature Genetics·W Gish, D J States
Aug 1, 1996·Trends in Genetics : TIG·J W Fickett
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
Apr 25, 1997·Journal of Molecular Biology·C Burge, S Karlin
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M G ReeseD Haussler
Oct 28, 1998·Bioinformatics·K Murakami, T Takagi
Apr 26, 2000·Genome Research·E Birney, R Durbin
Oct 24, 2000·Genome Research·R GuigóJ W Fickett
Jan 11, 2000·Nucleic Acids Research·K D Pruitt, D R Maglott
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
May 5, 2001·Genome Research·S RogicF B Ouellette
Jul 27, 2001·Bioinformatics·I KorfM R Brent
Dec 26, 2001·Nucleic Acids Research·M SakharkarS J de Souza
Feb 12, 2002·Bioinformatics·Vladimir PavlovićSimon Kasif
Sep 5, 2002·Nature Reviews. Genetics·Michael Q Zhang
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Jan 10, 2003·Nucleic Acids Research·Brigitte BoeckmannMichel Schneider
Jun 26, 2003·Nucleic Acids Research·Sylvain FoissacThomas Schiex
Oct 7, 2003·Annual Review of Genomics and Human Genetics·Jennifer L Ashurst, John E Collins
Jan 7, 2004·Genome Research·Jonathan E AllenSteven L Salzberg
Apr 2, 2004·Nature·A DunhamM T Ross
May 5, 2004·Genome Research·Ewan BirneyRichard Durbin

❮ Previous
Next ❯

Citations

Apr 14, 2005·International Journal for Parasitology·E A Worthey, P J Myler
Dec 16, 2006·Nucleic Acids Research·Keith Knapp, Yi-Ping Phoebe Chen
Aug 24, 2006·Genome Biology·David Carter, Richard Durbin
Aug 28, 2014·Briefings in Bioinformatics·Shipra GuptaDeepti D Deobagkar
Mar 31, 2009·Genomics, Proteomics & Bioinformatics·Xiao LiYizheng Zhang
Mar 18, 2017·PloS One·Vera OldratiReto Stöcklin

❮ 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.

© 2021 Meta ULC. All rights reserved