+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

AVID: A global alignment program



AVID: A global alignment program



Genome Research 13(1): 97-102



In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 010109618

Download citation: RISBibTeXText

PMID: 12529311

DOI: 10.1101/gr.789803


Related references

Super pairwise alignment (SPA): an efficient approach to global alignment for homologous sequences. Journal of Computational Biology 9(3): 477-486, 2002

The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment. Nucleic Acids Research 33(15): 4987-4994, 2005

Increasing the accuracy of the global alignment of amino acid sequences by constructing a set of alignment candidates. Biofizika 55(6): 965-975, 2010

Predicting Cervical Alignment Required to Maintain Horizontal Gaze Based on Global Spinal Alignment. Spine 41(23): 1795-1800, 2016

A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics 32(13): 1933-1942, 2016

Design and results of the antiarrhythmics vs implantable defibrillators (AVID) registry. The AVID Investigators. Circulation 99(13): 1692-1699, 1999

Simultaneous visualization of FDG avid and non-avid metastases in renal cell cancer. Revista Espanola de Medicina Nuclear e Imagen Molecular 31(6): 357-358, 2012

Global alignment, coordination and collaboration in perinatal research: the Global Obstetrics Network (GONet) Initiative. American Journal of Perinatology 30(3): 163-166, 2013

The AVID trial Evidence based or randomized control trials - is the AVID study too late?. American Journal of Cardiology 80(2): 194-197, 1997

Follow-up of patients with unexplained syncope and inducible ventricular tachyarrhythmias: Analysis of the AVID registry and an AVID substudy. Journal of Cardiovascular Electrophysiology 12(9): 996-1001, 2001

Therapeutic effect of avid and non-avid diphtheria sera. Annaly Mechnikov Skogo Instituta 6(1): 81-90, 1937

The AVID trial: evidence based or randomized control trials--is the AVID study too late? Antiarrhythmics Versus Implantable Defibrillators. American Journal of Cardiology 80(2): 194-197, 1997

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 20(10): 1546-1556, 2004

ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment. Computational Biology and Chemistry 33(3): 235-238, 2009

Follow-up of patients with unexplained syncope and inducible ventricular tachyarrhythmias: analysis of the AVID registry and an AVID substudy. Antiarrhythmics Versus Implantable Defibrillators. Journal of Cardiovascular Electrophysiology 12(9): 996-1001, 2001