PAI-IDA

[…] to allow the whole gi being captured. here we mainly discuss specific methods for gi detection., some gi detection methods combine multiple discrimination criteria, such as karlin's method and pai-ida . karlin's method and pai-ida predict gis and pais by evaluating multiple compositional features (gc content, dinucleotide frequencies, codon usage, and amino acid usage). karlin's method […]

[…] codon usage, mobility genes (including transposases and integrases), and trna genes [, ]. related tools using this kind of approach include alienhunter [], centroid [], gidetector [], gihunter [], pai ida [], and sigi-hmm []. comparative genome approach uses the phylogenetically close species as reference genomes and identifies subsequences that are unique in the query genomes and treats […]

[…] (v2.0.1) . tatp 1.0 server (v2.0) and tatfind 1.2 program were used to detect the potential substrates of the tat secretion system. pathogenicity islands and anomalous genes were detected by pai-ida and sigi-hmm , respectively., phylogenetic position of e. tarda eib202 within the enterobacteriaceae was determined based on the protein sequences of 44 housekeeping genes (adk, aroc, dnaa, […]