NDLI: The PARIGA Server for Real Time Filtering and Analysis of Reciprocal BLAST Results

Content Provider	PubMed Central
Author	Orsini, Massimiliano Simone, Carcangiu Cuccuru, Gianmauro Uva, Paolo Tramontano, Anna
Editor	Haslam, Niall James
Copyright Year	2013
Abstract	BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.
Related Links	http://dx.doi.org/10.1371/journal.pone.0062224
Starting Page	62224
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	5
Volume Number	8
Language	English
Publisher	Public Library of Science
Publisher Date	2013-05-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Div-BLAST: Diversification of Sequence Search Results

Real-Time Analysis and Visualization for Single-Molecule Based Super-Resolution Microscopy

A Reconfigurable Real-Time Compressive-Sampling Camera for Biological Applications

Real-Time PyMOL Visualization for Rosetta and PyRosetta

Quantitative Microplate Assay for Real-Time Nuclease Kinetics

Multicolor Combinatorial Probe Coding for Real-Time PCR

Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

Circadian Variation of the Human Metabolome Captured by Real-Time Breath Analysis

Real-Time Decision Fusion for Multimodal Neural Prosthetic Devices

The PARIGA Server for Real Time Filtering and Analysis of Reciprocal BLAST Results

Similar Documents

Div-BLAST: Diversification of Sequence Search Results

Real-Time Analysis and Visualization for Single-Molecule Based Super-Resolution Microscopy

A Reconfigurable Real-Time Compressive-Sampling Camera for Biological Applications

Real-Time PyMOL Visualization for Rosetta and PyRosetta

Quantitative Microplate Assay for Real-Time Nuclease Kinetics

Multicolor Combinatorial Probe Coding for Real-Time PCR

Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

Circadian Variation of the Human Metabolome Captured by Real-Time Breath Analysis

Real-Time Decision Fusion for Multimodal Neural Prosthetic Devices

The PARIGA Server for Real Time Filtering and Analysis of Reciprocal BLAST Results