Evaluation and improvements in the automatic alignment of protein sequences

G J Barton, M J Sternberg

Research output: Contribution to journalArticle

106 Citations (Scopus)

Abstract

The accuracy of protein sequence alignment obtained by applying a commonly used global sequence comparison algorithm is assessed. Alignments based on the superposition of the three-dimensional structures are used as a standard for testing the automatic, sequence-based methods. Alignments obtained from the global comparison of five pairs of homologous protein sequences studied gave 54% agreement overall for residues in secondary structures. The inclusion of information about the secondary structure of one of the proteins in order to limit the number of gaps inserted in regions of secondary structure, improved this figure to 68%. A similarity score of greater than six standard deviation units suggests that an alignment which is greater than 75% correct within secondary structural regions can be obtained automatically for the pair of sequences.

Original languageEnglish
Pages (from-to)89-94
Number of pages6
JournalProtein Science
Volume1
Issue number2
Publication statusPublished - 1 Feb 1987

Fingerprint

Sequence Alignment
Secondary Protein Structure
Sequence Homology
Proteins
Testing

Keywords

  • Algorithms
  • Amino Acid Sequence
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Engineering

Cite this

@article{3421b70e28174353b54b1f3d33a1fdc5,
title = "Evaluation and improvements in the automatic alignment of protein sequences",
abstract = "The accuracy of protein sequence alignment obtained by applying a commonly used global sequence comparison algorithm is assessed. Alignments based on the superposition of the three-dimensional structures are used as a standard for testing the automatic, sequence-based methods. Alignments obtained from the global comparison of five pairs of homologous protein sequences studied gave 54{\%} agreement overall for residues in secondary structures. The inclusion of information about the secondary structure of one of the proteins in order to limit the number of gaps inserted in regions of secondary structure, improved this figure to 68{\%}. A similarity score of greater than six standard deviation units suggests that an alignment which is greater than 75{\%} correct within secondary structural regions can be obtained automatically for the pair of sequences.",
keywords = "Algorithms, Amino Acid Sequence, Molecular Sequence Data, Protein Conformation, Protein Engineering",
author = "Barton, {G J} and Sternberg, {M J}",
year = "1987",
month = "2",
day = "1",
language = "English",
volume = "1",
pages = "89--94",
journal = "Protein Science",
issn = "0961-8368",
publisher = "Wiley",
number = "2",

}

Evaluation and improvements in the automatic alignment of protein sequences. / Barton, G J; Sternberg, M J.

In: Protein Science, Vol. 1, No. 2, 01.02.1987, p. 89-94.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Evaluation and improvements in the automatic alignment of protein sequences

AU - Barton, G J

AU - Sternberg, M J

PY - 1987/2/1

Y1 - 1987/2/1

N2 - The accuracy of protein sequence alignment obtained by applying a commonly used global sequence comparison algorithm is assessed. Alignments based on the superposition of the three-dimensional structures are used as a standard for testing the automatic, sequence-based methods. Alignments obtained from the global comparison of five pairs of homologous protein sequences studied gave 54% agreement overall for residues in secondary structures. The inclusion of information about the secondary structure of one of the proteins in order to limit the number of gaps inserted in regions of secondary structure, improved this figure to 68%. A similarity score of greater than six standard deviation units suggests that an alignment which is greater than 75% correct within secondary structural regions can be obtained automatically for the pair of sequences.

AB - The accuracy of protein sequence alignment obtained by applying a commonly used global sequence comparison algorithm is assessed. Alignments based on the superposition of the three-dimensional structures are used as a standard for testing the automatic, sequence-based methods. Alignments obtained from the global comparison of five pairs of homologous protein sequences studied gave 54% agreement overall for residues in secondary structures. The inclusion of information about the secondary structure of one of the proteins in order to limit the number of gaps inserted in regions of secondary structure, improved this figure to 68%. A similarity score of greater than six standard deviation units suggests that an alignment which is greater than 75% correct within secondary structural regions can be obtained automatically for the pair of sequences.

KW - Algorithms

KW - Amino Acid Sequence

KW - Molecular Sequence Data

KW - Protein Conformation

KW - Protein Engineering

M3 - Article

VL - 1

SP - 89

EP - 94

JO - Protein Science

JF - Protein Science

SN - 0961-8368

IS - 2

ER -