Abstract
Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation. Results: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 699-707 |
| Number of pages | 9 |
| Journal | Bioinformatics |
| Volume | 22 |
| Issue number | 6 |
| DOIs | |
| State | Published - Mar 15 2006 |
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ASJC Scopus subject areas
- Clinical Biochemistry
- Computer Science Applications
- Computational Theory and Mathematics
Cite this
OrthologID : Automation of genome-scale ortholog identification within a parsimony framework. / Chiu, Joanna C.; Lee, Ernest K.; Egan, Mary G.; Sarkar, Indra Neil; Coruzzi, Gloria M.; DeSalle, Rob.
In: Bioinformatics, Vol. 22, No. 6, 15.03.2006, p. 699-707.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - OrthologID
T2 - Automation of genome-scale ortholog identification within a parsimony framework
AU - Chiu, Joanna C.
AU - Lee, Ernest K.
AU - Egan, Mary G.
AU - Sarkar, Indra Neil
AU - Coruzzi, Gloria M.
AU - DeSalle, Rob
PY - 2006/3/15
Y1 - 2006/3/15
N2 - Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation. Results: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.
AB - Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation. Results: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.
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U2 - 10.1093/bioinformatics/btk040
DO - 10.1093/bioinformatics/btk040
M3 - Article
C2 - 16410324
AN - SCOPUS:33645106540
VL - 22
SP - 699
EP - 707
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 6
ER -