ESTMAP: a system for expressed sequence tags mapping on genomic sequences

IEEE Transactions on Nanobioscience
L Milanesi, I B Rogozin

Abstract

The completion of a number of large genome sequencing projects emphasizes the importance of protein-coding gene predictions. Most of the problems associated with gene prediction are caused by the complex exon-intron structures commonly found in eukaryotic genomes. However, information from homologous sequences can significantly improve the accuracy of the prediction. In particular, expressed sequence tags (ESTs) are very useful for this purpose, since currently existing EST collections are very large. We developed an ESTMAP system, which utilizes homology searches against a database of repetitive elements using the RepeatView program and the EST Division of GenBank using the BLASTN program. ESTMAP extracts "exact" matches with EST sequences (> 95% of homology) from BLASTN output file and predicts introns in DNA comparing ESTs and a query sequence. ESTMAP is implemented as a part of the WebGene system (http://www.cnr.it/webgene).

References

Oct 1, 1992·Journal of Molecular Evolution·J JurkaA Milosavljevic
Feb 13, 1992·Nature·M D AdamsJ C Venter
Jan 1, 1991·DNA Sequence : the Journal of DNA Sequencing and Mapping·K OkuboK Matsubara
Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M S Gelfand
Jun 1, 1994·Computer Applications in the Biosciences : CABIOS·X Huang
Sep 30, 1994·Science·M S BoguskiD E Bassett
Jun 1, 1996·Computer Applications in the Biosciences : CABIOS·I B RogozinN A Kolchanov
Sep 1, 1996·Genome Research·L D HillierM Marra
Apr 15, 1997·Nucleic Acids Research·T G Wolfsberg, D Landsman
Jul 1, 1997·Journal of Molecular Evolution·I B Rogozin, L Milanesi
Aug 1, 1997·Computer Applications in the Biosciences : CABIOS·R Mott
Feb 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·G VasmatzisI Pastan
Sep 17, 1999·Bioinformatics·L MilanesiI B Rogozin
Dec 30, 1999·Genome Research·A A MironovM S Gelfand
Jun 14, 2000·Current Opinion in Structural Biology·S LewisM G Reese
Sep 13, 2000·Nucleic Acids Research·F LiangJ Quackenbush
Jul 24, 2001·Briefings in Bioinformatics·I B RogozinL R Adkison
Jul 27, 2001·Briefings in Bioinformatics·C V Jongeneel

❮ Previous
Next ❯

Citations

Oct 26, 2005·BMC Bioinformatics·Alexander ChurbanovHesham Ali
Feb 7, 2006·Current Opinion in Biotechnology·Aaron J Windsor, Thomas Mitchell-Olds

❮ 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.