XSAnno: A Framework to Generate Orthologous Annotation in Cross-species Comparison

We developed a computational framework to make ortholog annotation between closely related species, through whole genome alignment and local sequence alignment followed by multiple filters. The annotation is designed for cross-species transcriptome comparisons using RNA sequencing data, but can also be applied to gene prediction for species with incomplete annotation. Here we tested the previous methods in comparing brain transcriptomes of human and closely related non-human primates (chimpanzee and rhesus macaque), our approach expands ortholog annotation and reduces the false discovery of differentially expressed genes, while keeping the false negative rate low. Additional data and software updates will be incorporated into the database as it becomes available

Pre-process Data Publicly Available ( Readme )

1.   Ensembl v64 Human-Chimpanzee
2.   Ensembl v64 Human-Macaque
3.   Gencode v10 Human-Chimpanzee
4.   Gencode v10 Human-Macaque
5.   Gencode v10 Human-Chimpanzee-Macaque

Standalone Source Code Publicly Available

9/24/2013: Version 1 released
     Download source code

Please send questions and comments to mingfeng.li@yale.edu