The family based variability in protein family expansion
Sarkar, Anasua LU
; Nikolski, Macha
and Durrens, Pascal
(2013)
In International Journal of Bioinformatics Research and Applications
9(2).
p.121-133
- Abstract
In this paper we propose an automatic protein family expansion approach for recruitment of new members among the protein-coding genes in newly sequenced genomes. The criteria for adding a new member to a family depends on the structure of each individual family versus being globally uniform. The detection of a threshold in the ROC space of all sorted iterative profile sets defines the alignments selection criteria for each family. Furthermore, the statistical estimation of most-frequent optimal sorting criteria generates the optimal filtering strategy in a learning-parameter set for profile-based homology search.
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/a981bf24-9c35-4461-bdc8-7236489d8aa2
- author
- Sarkar, Anasua
LU
; Nikolski, Macha
and Durrens, Pascal
- publishing date
- 2013-04-05
- type
- Contribution to journal
- publication status
- published
- keywords
- Alignment selection criteria, Optimal filtering strategy, Protein family expansion, Protein specific scoring matrix, Remote homologues, ROC analysis, Sequence profile
- in
- International Journal of Bioinformatics Research and Applications
- volume
- 9
- issue
- 2
- pages
- 121 - 133
- publisher
- Inderscience Publishers
- external identifiers
-
- pmid:23467059
- scopus:84875650910
- ISSN
- 1744-5485
- DOI
- 10.1504/IJBRA.2013.052473
- language
- English
- LU publication?
- no
- id
- a981bf24-9c35-4461-bdc8-7236489d8aa2
- date added to LUP
- 2018-10-09 09:54:36
- date last changed
- 2025-10-14 12:39:17
@article{a981bf24-9c35-4461-bdc8-7236489d8aa2,
abstract = {{<p>In this paper we propose an automatic protein family expansion approach for recruitment of new members among the protein-coding genes in newly sequenced genomes. The criteria for adding a new member to a family depends on the structure of each individual family versus being globally uniform. The detection of a threshold in the ROC space of all sorted iterative profile sets defines the alignments selection criteria for each family. Furthermore, the statistical estimation of most-frequent optimal sorting criteria generates the optimal filtering strategy in a learning-parameter set for profile-based homology search.</p>}},
author = {{Sarkar, Anasua and Nikolski, Macha and Durrens, Pascal}},
issn = {{1744-5485}},
keywords = {{Alignment selection criteria; Optimal filtering strategy; Protein family expansion; Protein specific scoring matrix; Remote homologues; ROC analysis; Sequence profile}},
language = {{eng}},
month = {{04}},
number = {{2}},
pages = {{121--133}},
publisher = {{Inderscience Publishers}},
series = {{International Journal of Bioinformatics Research and Applications}},
title = {{The family based variability in protein family expansion}},
url = {{http://dx.doi.org/10.1504/IJBRA.2013.052473}},
doi = {{10.1504/IJBRA.2013.052473}},
volume = {{9}},
year = {{2013}},
}