Sentence examples for minimum bit score from inspiring English sources

We set the parameters to utilize the BLOSUM62 matrix and a minimum bit score of 30, and we required that the BLAST alignment cover at least 50% of both proteins.

These mutation events may reflect accumulation of point mutations, or occurrence of sites where retrotransposons insert within preexisting retrotransposons to create interrupted sequences of retroelements [42] – such that alignments do not exceed minimum bit score thresholds.

Our E value cutoff created a minimum bit score of 74 which is more stringent that the minimum bit score of 50 which was used by Tsai and co-workers [ 45].

In contrast, when using less strict blastp hits with minimum bit score of 100, one obtains 144 singletons.

In addition, singletons with a minimum bit score of 45 to a UniRef90 cluster [ 37] (http://www.uniprot.org) were included.

First, homologous proteins from other species were searched using blastp against a non-redundant (nr) database (minimum bit score threshold 50; match length 20 amino acids).

According to a simulation experiment (Additional file 5: Figure S3A) minimum bit scores thresholds of 148, 110, and 74 can be used for phylogenetic and functional assignments at genus level (with >80% confidence level), phylogenetic and functional assignment at family level (with >80% confidence level), and for a reliable function (COG) assignment (with > 95% confidence level), respectively.

Unassigned mRNA reads were further analyzed by a BLASTX to the complete NCBI protein database, protein sequences of the MetaHIT database [ 35] and human small intestinal metagenome databases [ 4] using a minimum bit-score of 40 (Additional file 5: Figure S3B).

The mRNA reads phylogenetic profiling at genus level was done with reads with a minimum bit alignment score of 148.

The second step was performed on the remaining reads using BLASTN with a minimum alignment bit score of 54 using a filtering database consisting of complete ribosomal RNA loci, and tRNA sequences of bacteria, archaea and eukaryota taken from the NCBI and SILVA [ 54] databases.

The successful reads were BLAST-ed against the DEOP gene database (Bit score 50, minimum percentage identity 60%) and mapped to DEOP pathways.