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The proteins sequences were then clustered together using a global identity threshold of 95% and a gap penalty of 20 using usearch [ 43] to retrieve the longest sequence of each cluster.
Of them, 24,487 and 19,212 similar contigs were clustered into 4869 and 2633 clusters by TGICL [ 15] using a default threshold of 0.94 and CD-HIT [ 16] using a global identity threshold of 0.90.
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Once filtered to remove highly homologous sequences (>90% sequence identity), the relative specificity of the initial profiles was tested by scanning all included LmSIDER sequences with both HMM profiles using a global alignment algorithm (Additional file 2).
In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment.
For the PpaV2 sequence set the program cd-hit-est [ 20] was used to find all ORFs that had a global identity of > 80% with S. cerevisiae.
We are the middle of a global identity crisis.
A global identity could offer the base on which different micro-identities would be tied together.
A global identity cutoff of 80% was applied to all read matches, from which reads with high identity to reference genomes were kept.
I use a global palette.
(i) Identity Spoofing Attempting to gain access to information service by using a false identity.
Identities were calculated using a Percent Identity Matrix created by Clustal 2.0.12.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com