ortholog identification
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2018 ◽  
Vol 35 (4) ◽  
pp. 546-552 ◽  
Author(s):  
Justin B Miller ◽  
Brandon D Pickett ◽  
Perry G Ridge

2013 ◽  
Vol 41 (W1) ◽  
pp. W242-W248 ◽  
Author(s):  
Cyrus Afrasiabi ◽  
Bushra Samad ◽  
David Dineen ◽  
Christopher Meacham ◽  
Kimmen Sjölander

2011 ◽  
Vol 12 (5) ◽  
pp. 413-422 ◽  
Author(s):  
K. Sjolander ◽  
R. S. Datta ◽  
Y. Shen ◽  
G. M. Shoffner

2010 ◽  
Vol 10 (1) ◽  
pp. 343 ◽  
Author(s):  
Ajanthah Sangaralingam ◽  
Edward Susko ◽  
David Bryant ◽  
Matthew Spencer

2008 ◽  
Vol 06 (04) ◽  
pp. 811-824 ◽  
Author(s):  
ALEXANDER E. IVLIEV ◽  
MARINA G. SERGEEVA

The identification of orthologs to a set of known genes is often the starting point for evolutionary studies focused on gene families of interest. To date, the existing orthology detection tools (COG, InParanoid, OrthoMCL, etc.) are aimed at genome-wide ortholog identification and lack flexibility for the purposes of case studies. We developed a program OrthoFocus, which employs an extended reciprocal best hit approach to quickly search for orthologs in a pair of genomes. A group of paralogs from the input genome is used as the start for the forward search and the criterion for the reverse search, which allows handling many-to-one and many-to-many relationships. By pairwise comparison of genomes with the input species genome, OrthoFocus enables quick identification of orthologs in multiple genomes and generates a multiple alignment of orthologs so that it can further be used in phylogenetic analysis. The program is available at .


2006 ◽  
Vol 22 (6) ◽  
pp. 699-707 ◽  
Author(s):  
J. C. Chiu ◽  
E. K. Lee ◽  
M. G. Egan ◽  
I. N. Sarkar ◽  
G. M. Coruzzi ◽  
...  

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