Author: Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.
Title: A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species Document date: 2019_6_4
ID: telmxmp4_10
Snippet: Building Orthologous Gene Families. The search for orthologous genes was performed in two primary steps. First, we searched for orthologs in the genomic datasets. With genomic data, one is able to use syntenic information to help predict orthology. We used all-v-all BLAST reciprocal best hits of the protein sequences, filtered using three sources of syntenic information: public orthology predictions from BioMart, proximity via whole genome alignm.....
Document: Building Orthologous Gene Families. The search for orthologous genes was performed in two primary steps. First, we searched for orthologs in the genomic datasets. With genomic data, one is able to use syntenic information to help predict orthology. We used all-v-all BLAST reciprocal best hits of the protein sequences, filtered using three sources of syntenic information: public orthology predictions from BioMart, proximity via whole genome alignment, and proximity of similar neighboring genes (43) (44) (45) . Second, we searched for orthologs in transcriptomic datasets. We selected the best BLAST reciprocal best hits in transcriptomic data against genes found in the genomic orthologous gene sets, filtered by search using HMMER (46) , a hidden Markov model-based homology search software package, and filtered by match length (Methods).
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