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PAI-IDA specifications


Unique identifier OMICS_08279
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No


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PAI-IDA citations


Computational methods for predicting genomic islands in microbial genomes

PMCID: 4887561
PMID: 27293536
DOI: 10.1016/j.csbj.2016.05.001

[…] 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 […]


A Computational Framework for Tracing the Origins of Genomic Islands in Prokaryotes

PMCID: 4897231
PMID: 27433520
DOI: 10.1155/2014/732857

[…] 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 […]


Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

PMCID: 2764856
PMID: 19865481
DOI: 10.1371/journal.pone.0007646

[…] (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, […]

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PAI-IDA institution(s)
Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

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