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- Homo sapiens
- Mus musculus
- Rattus norvegicus
Publication for BBH-LS
Altered expression profiles of microRNA families during de etiolation of maize and rice leaves
[…] y.cau.edu.cn/PlantGSEA/). Conserved lncRNAs were predicted by the following steps: (1) Identifying ortholog gene pairs that are syntenically conserved across Z. mays, O. sativa and Setaria italica by BBH-LS with default parameters ; (2) aligning the intergenic regions between ortholog gene pair with BLAST setting e-value cutoff to be 1e−6 ; (3) checking if any reads were mapped to this region […]
Systems analysis of cis regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de etiolation
[…] y a combination of tools including BBH-LS (), orthoMCL (), Inparanoid (), MSOAR2 (), and the Ensembl database (). The results were organized based on the following principles. First, the results from BBH-LS, which is the most stringent method (), were used as the basis. Second, if a particular ortholog pair was not reported by BBH-LS but was by other methods, we retained the results of the other m […]
Stringent homology based prediction of H. sapiens M. tuberculosis H37Rv protein protein interactions
[…] PIs). Therefore when predicting the H. sapiens–M. tuberculosis H37Rv PPIs we only need to identify the prokaryotic homologs between template and targeted species in this situation. We identify, using BBH-LS (strength threshold β≥0.01), the homologs between M.tuberculosis H37Rv and the 10 bacteria from the PATRIC database. Here in this work we use the “consensus score” (the number of supporting tem […]
Modelling biological systems from molecules to dynamical networks
[…] that identifying corresponding genes (orthologs) in different species is an important step in genome-wide comparative analysis. Melvin Zhang and Hon Wai Leong presented a simple yet effective method (BBH-LS) for the identification of positional homologs from the comparative analysis of two genomes and integrated sequence similarity and gene context similarity in order to get more accurate ortholog […]
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