Genes within a single genome can be classified as singletons, dispersed duplicates, proximal duplicates, tandem duplicates and segmental/WGD duplicates depending on their copy number and genomic distribution. The following procedure is used to assign gene classes: (i) All genes are initially classified as ‘singletons’ and assigned gene ranks according to their order of appearance along chromosomes; (ii) BLASTP results are evaluated and the genes with BLASTP hits to other genes are re-labeled as ‘dispersed duplicates’; (iii) In any BLASTP hit, the two genes are re-labeled as ‘proximal duplicates’ if they have a difference of gene rank<20 (configurable); (iv) In any BLASTP hit, the two genes are re-labeled as ‘tandem duplicates’ if they have a difference of gene rank = 1; (v) MCScanX is executed. The anchor genes in collinear blocks are re-labeled as ‘WGD/segmental’. So, if a gene appears in multiple BLASTP hits, it will be assigned a unique class according to the order of priority: WGD/segmental>tandem>proximal>dispersed.
Protocol detail
Genome-Wide Gene Duplication Classification
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization :
Other organizations : University of Georgia, North China University of Science and Technology, J. Craig Venter Institute
Top 5 similar protocols
Protocol cited in 495 other protocols
Variable analysis
independent variables
- Gene rank order along chromosomes
- BLASTP hits to other genes
- Difference of gene rank (configurable, <20 for proximal duplicates, =1 for tandem duplicates)
- Execution of MCScanX to identify anchor genes in collinear blocks
- Gene classification (singletons, dispersed duplicates, proximal duplicates, tandem duplicates, WGD/segmental duplicates)
- Not explicitly mentioned
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!