Criteria for identifying tandem and segmental duplicates
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7.2 years ago
kozhaki.seq ▴ 60

There are previous reports available on the estimated  tandem and segmental  duplicated genes (TDs and SDs) in rice ( http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063551). But I am not sure about the  reliability of  the data.Hence,I would like to analyze TDs and SD genes (not blocks) in rice.

Here, I am unable to make a criteria for TD and SD estimation (a condition which gives better reliable data). I noticed different groups used their-own criteria. For ex,  the previous work uses "identity was > = 30% and the alignment covered > = 70% of the protein length" for TD. In other work, > 94% identity is used for SD (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179966/)

1. Can anyone give suggestion before my analysis? I mean a cut off for TDs and SDs identification separately.

2. If anyone know a software suit which deals such duplicated genes estimation, it would be helpful. (FYI: I found some published suits, but the webpage is not working).

 

Thank you.

 

 

 

genome blast alignment duplication software • 2.0k views
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Entering edit mode
6.8 years ago
Hranjeev ★ 1.5k

The typical criteria that defines a segmental duplication is that the sequence is at least 1kb and 90% identical to the duplicate.

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