Sentence examples for gathering thresholds from inspiring English sources

Alignment scores above the Pfam gathering thresholds were counted significant.

HMMER 3 [ 41] with gathering thresholds was used to annotate the samples with Pfam domains.

However, the alignment scores were in most cases below the Pfam gathering thresholds.

Using manually curated cutoff scores (gathering thresholds) provided in Pfam domain HMM files, no uORFs returned significant hits to any domain.

For Pfam, the family-specific thresholds from the Pfam database (gathering thresholds) were used if they were stricter than our default threshold.

The pfam_scan program was used in default mode (–cut_ga option that uses the family-specific Pfam gathering thresholds to establish significance).

For the annotation of Pfam-A domains, we used the model-defined gathering threshold and query sequences were required to match at least 30% of the defining model58.

Please note that no bit score threshold is used here, but the default HMMER gathering threshold for ZF domains is 17.7, so you can decide to select only confident ZF domains with bit scores exceeding 17.7.

A protein is taken to contain a domain if its E-value exceeds the domain-specific Pfam-defined gathering threshold.

This indicates that the level of similarity to this domain is weaker in this protein (below the gathering threshold used in the construction of PFAM families).

Putative functions were assigned by domain composition after scanning the sequences against Pfam [45] using the gathering threshold as cut-off.