Weighting aligned protein or nucleic acid sequences to correct for unequal representation

Aligned sequences from the same family (e.g. the haemoglobins) are seldom representative of the entire family. This is because (1) the sequence databases are heavily skewed toward a small number of organisms and (2) only a minute fraction of all the different family members have been sequenced. For...

Full description

Saved in:
Bibliographic Details
Published inJournal of molecular biology Vol. 216; no. 4; pp. 813 - 818
Main Authors Sibbald, Peter R., Argos, Patrick
Format Journal Article
LanguageEnglish
Published Oxford Elsevier Ltd 20.12.1990
Elsevier
Subjects
Algorithms
Amino Acid Sequence
Animals
Base Sequence
Biological and medical sciences
Diverse techniques
Fundamental and applied biological sciences. Psychology
Globins
Molecular and cellular biology
Molecular Sequence Data
Nucleoside-Phosphate Kinase - genetics
Thymidine Kinase - genetics
Viruses - genetics
Performance evaluation
Proteins
Organism
Weighting
Sequence alignment
Database
Method
Phylogeny
Nucleic acid
Aminoacid sequence
Online AccessGet full text

Cover

More Information
Summary:Aligned sequences from the same family (e.g. the haemoglobins) are seldom representative of the entire family. This is because (1) the sequence databases are heavily skewed toward a small number of organisms and (2) only a minute fraction of all the different family members have been sequenced. For many applications, such as using alignments or profiles to perform database searches for distantly related family members, such unequal representation requires correction. An algorithm to perform appropriate weighting of individual sequences is presented along with examples illustrating its efficacy.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0022-2836
1089-8638
DOI:10.1016/S0022-2836(99)80003-5