The abbreviations used are:

CoordinatesCoordinates of the gene
StrandStrand
LengthLength of the sequence in bp
PIDNumber code of the gene
Gene nameGene name
SynonymSynonym gene name
FunctionCodeFunctional classification of the gene according with the Cluster of Ortologous Genes (COG) database
COGCOG family that the gene belong
GCRegion"-" indicates that the gene belong to a region with a low G+C content; "+" indicates that the gene belong to a region with a high G+C content.
"f" indicates that the gene has been filtered and it is not predicted as being acquired or not acquired
HGT"H" indicates a potential horizontally transferred gene and "f" indicates that the gene has been filtered and it is not predicted as being acquired or not acquired
FunctionFunction of the gene
GC1G+C content of first codon position
SD1Number of Standard Deviations (SD) from G+C1 mean
Sim1"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
GC2G+C content of second codon position
SD2Number of Standard Deviations (SD) from G+C2 mean
Sim2"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
GC3G+C content of third codon position.
SD3Number of Standard Deviations (SD) from G+C3 mean
Sim3"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
GCTTotal G+C content.
SDTNumber of Standard Deviations (SD) from G+CT mean
SimT"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
SimGC"1" indicates potential "odd" gene in the G+C content; "2" indicates "odd" gene in the G+C content.
MahMahalanobis distance of the gene.
SimMah"1" indicates potencial "odd" gene in the codon usage; "2" indicates "odd" gene in the codon usage
Dev.AAAmino acids whose content deviates more than 3SD from the mean content and number of SD

Others abbreviations used in the correspondence analysis of relative synonymous codon usage are:

Nc Effective number of codons (Wright 1990. Gene 87, 23-29). Gives the number of equally used codons which would generate the same codon usage bias as observed. A gene utilizing only one codon per amino acid has the strongest bias and the minimum index value (20). A gene using all codons equally has a value of 61.
P2 Translational efficiency (Gouy and Gautier 1982. NAR 10, 7055-7074). Describes the proportion of codons conforming to the intermediate strength of codon-anticodon interaction energy rule of Grosjean and Fiers. It goes between 0 i 1.
ICDI Intrinsec codon bias index (ICDI) (Freire-Picos et al. 1994. Gene 139, 43-49). Range between 0 for non biassed and 1 for biassed genes.
Chi2 Scaled Chi2 (Shileds and Sharp 1987. NAR 15, 8023-8040). This index messures the degree of bias due to a non uniformous use of synomous codons of a gene, using uniform synonymous codon usage as the expectation.

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