Bioinformatics. 2004 Apr 12;20(6):974-5. Epub 2004 Feb 5.

SQUARE--determining reliable regions in sequence alignments.

Source

CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain. mtress@gredos.cnb.uam.es

Abstract

The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.

PMID:: 14764569; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

Proteins

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Molecular Biology Databases

TreeDet - Bioinformatics.ca Links Directory

Supplemental Content

Related citations

The SSEA server for protein secondary structure alignment. [Bioinformatics. 2005]
The SSEA server for protein secondary structure alignment.
Fontana P, Bindewald E, Toppo S, Velasco R, Valle G, Tosatto SC. Bioinformatics. 2005 Feb 1; 21(3):393-5. Epub 2004 Sep 3.
Predicting reliable regions in protein alignments from sequence profiles. [J Mol Biol. 2003]
Predicting reliable regions in protein alignments from sequence profiles.
Tress ML, Jones D, Valencia A. J Mol Biol. 2003 Jul 18; 330(4):705-18.
Using Dali for structural comparison of proteins. [Curr Protoc Bioinformatics. 2006]
Using Dali for structural comparison of proteins.
Holm L, Kääriäinen S, Wilton C, Plewczynski D. Curr Protoc Bioinformatics. 2006 Jul; Chapter 5:Unit 5.5.
Review Bioinformatics methods to predict protein structure and function. A practical approach. [Mol Biotechnol. 2003]
Review Bioinformatics methods to predict protein structure and function. A practical approach.
Edwards YJ, Cottage A. Mol Biotechnol. 2003 Feb; 23(2):139-66.
Review Rapid retrieval of protein structures from databases. [Drug Discov Today. 2007]
Review Rapid retrieval of protein structures from databases.
Aung Z, Tan KL. Drug Discov Today. 2007 Sep; 12(17-18):732-9. Epub 2007 Aug 28.

See reviews... See all...

Cited by 5 PubMed Central articles

firestar--advances in the prediction of functionally important residues. [Nucleic Acids Res. 2011]
firestar--advances in the prediction of functionally important residues.
Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W235-41. Epub 2011 Jun 14.
Determination and validation of principal gene products. [Bioinformatics. 2008]
Determination and validation of principal gene products.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, et al. Bioinformatics. 2008 Jan 1; 24(1):11-7. Epub 2007 Nov 15.
firestar--prediction of functionally important residues using structural templates and alignment reliability. [Nucleic Acids Res. 2007]
firestar--prediction of functionally important residues using structural templates and alignment reliability.
López G, Valencia A, Tress ML. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W573-7. Epub 2007 Jun 21.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

SQUARE--determining reliable regions in sequence alignments.
SQUARE--determining reliable regions in sequence alignments.
Bioinformatics. 2004 Apr 12 ;20(6):974-5. Epub 2004 Feb 5 .

PubMed
Impact of clinical alerts within an electronic health record on routine childhoo...
Impact of clinical alerts within an electronic health record on routine childhood immunization in an urban pediatric population.
Pediatrics. 2007 Oct ;120(4):707-14.

PubMed
Regulation of TNF-alpha-activated PKC-zeta signaling by the human biliverdin red...
Regulation of TNF-alpha-activated PKC-zeta signaling by the human biliverdin reductase: identification of activating and inhibitory domains of the reductase.
FASEB J. 2007 Dec ;21(14):3949-62. Epub 2007 Jul 17 .

PubMed
Impacts of informal caregiver availability on long-term care expenditures in OEC...
Impacts of informal caregiver availability on long-term care expenditures in OECD countries.
Health Serv Res. 2004 Dec ;39(6 Pt 2):1971-92.

PubMed
Effects of nattokinase, a pro-fibrinolytic enzyme, on red blood cell aggregation...
Effects of nattokinase, a pro-fibrinolytic enzyme, on red blood cell aggregation and whole blood viscosity.
Clin Hemorheol Microcirc. 2006 ;35(1-2):139-42.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: