Identification of conserved gene clusters in multiple genomes based on synteny and homology
Sarkar, Anasua LU
; Soueidan, Hayssam
and Nikolski, Macha
(2011)
In BMC Bioinformatics
12(Suppl. 9).
- Abstract
Background: Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams.Results: Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete... (More)
Background: Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams.Results: Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.Conclusions: The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.
(Less)
- author
- Sarkar, Anasua
LU
; Soueidan, Hayssam
and Nikolski, Macha
- publishing date
- 2011-10-05
- type
- Contribution to journal
- publication status
- published
- in
- BMC Bioinformatics
- volume
- 12
- issue
- Suppl. 9
- article number
- S18
- publisher
- BioMed Central (BMC)
- external identifiers
-
- pmid:22151970
- scopus:80053496177
- ISSN
- 1471-2105
- DOI
- 10.1186/1471-2105-12-S9-S18
- language
- English
- LU publication?
- no
- id
- 43120ad8-19b3-454d-a9c8-4c8378c1928e
- date added to LUP
- 2018-10-09 09:56:37
- date last changed
- 2024-03-18 15:58:42
@article{43120ad8-19b3-454d-a9c8-4c8378c1928e,
abstract = {{<p>Background: Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams.Results: Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.Conclusions: The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.</p>}},
author = {{Sarkar, Anasua and Soueidan, Hayssam and Nikolski, Macha}},
issn = {{1471-2105}},
language = {{eng}},
month = {{10}},
number = {{Suppl. 9}},
publisher = {{BioMed Central (BMC)}},
series = {{BMC Bioinformatics}},
title = {{Identification of conserved gene clusters in multiple genomes based on synteny and homology}},
url = {{http://dx.doi.org/10.1186/1471-2105-12-S9-S18}},
doi = {{10.1186/1471-2105-12-S9-S18}},
volume = {{12}},
year = {{2011}},
}