NCBI BLAST+ integrated into Galaxy

GigaScience
Peter J A CockNicola Soranzo

Abstract

The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows. The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible. This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.

Associated Datasets

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 9, 2002·Genome Research·Jason E StajichEwan Birney
Jun 25, 2004·Nucleic Acids Research·Aron Marchler-Bauer, Stephen H Bryant
Jan 24, 2007·Bioinformatics·Arthur L DelcherSteven L Salzberg
Aug 12, 2008·Bioinformatics·R C G HollandM J Schreiber
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 14, 2010·Current Protocols in Molecular Biology·Daniel BlankenbergJames Taylor
May 27, 2010·Nucleic Acids Research·Carole A GobleDavid De Roure
Aug 27, 2010·Bioinformatics·Naohisa GotoToshiaki Katayama
Nov 27, 2010·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Dec 15, 2010·Biotechnology Journal·Michael Fischbach, Christopher A Voigt
Jan 19, 2011·BMC Bioinformatics·Enis AfganJames Taylor
Jan 11, 2011·Bioinformatics·Oliver KellerStephan Waack
Jan 5, 2013·Journal of Biomedical Semantics·Mikel Egaña ArangurenMark D Wilkinson
Jun 14, 2013·BMC Genomics·Jeremy GoecksJames Taylor
Sep 3, 2013·Bioinformatics·Jan GrauStefan Posch
Mar 4, 2014·Bioinformatics·Daniel BlankenbergAnton Nekrutenko
Mar 13, 2014·Bioinformatics·Gianmauro CuccuruGiorgio Fotia
Mar 20, 2014·Bioinformatics·Torsten Seemann
Apr 22, 2014·Journal of the American Chemical Society·Andreas PrägMichael Müller
May 7, 2014·Nucleic Acids Research·Fidel RamírezThomas Manke
Jul 9, 2014·Genome Biology·Daniel BlankenbergAnton Nekrutenko
Oct 11, 2014·Journal of Proteome Research·Pratik D JagtapTimothy J Griffin

❮ Previous
Next ❯

Citations

Oct 30, 2015·Journal of Proteome Research·Kenneth VerheggenMarc Vaudel
Mar 12, 2005·BMC Genetics·Aaron C BrownDerry C Roopenian
Jun 18, 2005·BMC Bioinformatics·Liisa B KoskiGertraud Burger
Oct 28, 2015·BMC Pulmonary Medicine·Michael PhelippeauMichel Drancourt
Mar 14, 2018·Genome Génome / Conseil National De Recherches Canada·Alasdair T M HubbardColin G Fink
May 24, 2018·GigaScience·Bérénice BatutPierre Peyret
Aug 31, 2018·Genome Biology and Evolution·Peter ThorpeJorunn I B Bos
Feb 26, 2019·The Plant Journal : for Cell and Molecular Biology·Paul FourounjianJoachim Messing
May 30, 2019·American Journal of Physiology. Regulatory, Integrative and Comparative Physiology·Nicholas C WuCraig E Franklin
Jun 12, 2019·International Journal of Systematic and Evolutionary Microbiology·Arnau Casanovas-MassanaElsio A Wunder
Jan 24, 2020·G3 : Genes - Genomes - Genetics·Ryan BracewellDoris Bachtrog
Apr 18, 2020·The Journal of Antimicrobial Chemotherapy·François CamélénaUNKNOWN IAME Resistance Group
Sep 17, 2019·ELife·Ryan BracewellDoris Bachtrog
Nov 2, 2019·International Journal of Molecular Sciences·Riccardo Concu, M Natália D S Cordeiro
Jan 4, 2020·Microbiology and Molecular Biology Reviews : MMBR·Giorgio GabarriniJan Maarten van Dijl
Nov 2, 2019·Applications in Plant Sciences·Muhammad AhmadEva Maria Sehr
May 24, 2018·Nucleic Acids Research·Enis AfganDaniel Blankenberg
Jun 6, 2019·Archives of Virology·Mathieu MahillonAnne Legrève

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR

Software Mentioned

Galaxy Visual Analysis Framework
Docker
Perl scripts
TBLASTX
Docker Image
blastdbcmd
BLAST BLAST BLAST ( BLAST
BLAST +
BioJava
Galaxy Data Manager

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.