PMID: 11331235May 2, 2001Paper

Retrieval and on-the-fly alignment of sequence fragments from the HIV database

Bioinformatics
Brian GaschenB Foley

Abstract

The amount of HIV-1 sequence data generated (presently around 42000 sequences, of which more than 22000 are from the V3 region of the viral envelope) presents a challenge for anyone working on the analysis of these data. A major problem is obtaining the region of interest from the stored sequences, which often contain but are not limited to that region. In addition, multiple alignment programs generally cannot deal with the large numbers of sequences that are available for many HIV-1 regions. We set out to provide our users with a tool that will retrieve and create an initial alignment of the HIV sequences that are available for a given genomic region. The MPAlign (Multiple Pairwise Alignment) web interface is a collection of Perl scripts that retrieves sequences from the Los Alamos HIV sequence database based on a number of search parameters. All sequences were pairwise-aligned to a model sequence using the Hidden Markov Model-based program HMMER. The HMMER model is general enough to accommodate virtually all HIV-1 sequences stored in the database. To create a multiple sequence alignment, gaps were inserted into the sequences during retrieval, so that they are aligned to one another. Retrieving and aligning the almost 560 gp12...Continue Reading

Citations

Apr 24, 2010·Archives of Virology·Carlos A LopezEric Lorenzo
Sep 21, 2004·Bioinformatics·Carla KuikenRussell Richardson
Nov 9, 2011·Nucleic Acids Research·Carla KuikenHyejin Yoon
Jun 12, 2013·Nucleic Acids Research·Timothy I Shaw, Ming Zhang
May 17, 2013·Proceedings. Biological Sciences·Duncan PalmerGil McVean
Sep 15, 2005·HIV Medicine·E LospitaoA Holguín
Sep 5, 2008·Annual Review of Genomics and Human Genetics·Xiaonan YangGuo-Ping Zhao
Jan 30, 2004·Annual Review of Medicine·John W Shiver, Emilio A Emini
Mar 5, 2010·BMC Bioinformatics·Aridaman Pandit, Somdatta Sinha
Feb 10, 2007·BMC Evolutionary Biology·Karin S Dorman
Aug 16, 2011·Virology Journal·Muhammad Z YousafUsman A Ashfaq
Oct 5, 2013·AIDS Research and Human Retroviruses·Doris G RansyHugo Soudeyns
Sep 13, 2003·APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica·Lars E ErikssonKerstin I Falk
Mar 10, 2016·Journal of Chemical Information and Modeling·Alejandro Speck-PlancheM N D S Cordeiro
Nov 20, 2009·Virology·Avishek NandiUNKNOWN NIAID Center for HIV/AIDS Vaccine Immunology
Jul 14, 2006·BMC Bioinformatics·Randi VitaAlessandro Sette
Mar 10, 2015·AIDS Research and Human Retroviruses·Chandra Nath RoyHitoshi Oshitani
Oct 7, 2008·The International Journal of Biochemistry & Cell Biology·Hiroki NishikawaMasao Matsuoka
Feb 18, 2006·Biochimica Et Biophysica Acta·Miguel R MorenoJosé Villalaín
Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Hiromi ImamichiH Clifford Lane
Jan 12, 2007·Antiviral Research·Lilly K W YuenAngeline Bartholomeusz
Aug 17, 2016·BMC Microbiology·Evan W FlodenMartin Pospíšek
Sep 30, 2016·PloS One·Amirhossein ManzourolajdadJohn L Spouge
Jul 14, 2007·Antiviral Chemistry & Chemotherapy·Peter T HraberUNKNOWN Los Alamos HIV database team
Mar 18, 2015·Viruses·Livia Maria Gonçalves RossiPaula Rahal

❮ 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.