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CBS >> CBS Prediction Servers >> GenomeAtlas >> Overrep. Oligomers for strain ,

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Selection summary: 4 segments, 1 strain, 1 species, 1 genus

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The data clustering tool makes use of the CBS Genome Atlas Database. Please cite
the references below if you are including these results in your scientific work

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REFERENCES:

Peter F. Hallin and David Ussery (2004). CBS Genome Atlas Database: A dynamic storage for bioinformatic results and sequence data Bioinformatics 20:3682-3686 PDF | Pubmed
Hanni Willenbrock, Tim T. Binnewies, Peter F. Hallin, and David W. Ussery (2005). Genome Update: 2D Clustering of Bacterial Genomes Microbiology 151:333-336

CORRESPONDENCE:

Scientific questions: David W. Ussery Peter Fischer Hallin Hans-Henrik Staerfeldt

This file is last modified Thursday 12th of February 2009 12:54:46 GMT2D Clustering witn has been accessed 159,354 times since 2004-12-23 01:00:23Total hits for all related pages has been accessed 3,617,491 times since 2004-03-23 14:54:29

# primary and alternative sigma factors (SIGMA70_PROMOTERS_COUNT)
A content (ACONTENT)
AT content (ATCONTENT)
AT Skew (AT_SKEW_LEADOVERLAG)
Avg Nucleosomal position preference (TRAVERS_AVG)
Avg. DNA Curvature (using 21 bp window) (CURVATURE_AVG)
Avg. DNA melting energy (kcal/mol) (ORNSTEIN_AVG)
Avg. DNA Propeller Twist (ELHASSAN_AVG)
Avg. DNase I Sensitivity (BRUKNER_AVG)
Avg. Protein Deformability (OLSON_AVG)
C content (CCONTENT)
Coding Density / bp pr. gene (BPPRGENE)
Doubling Time (DOUBLING_TIME)
Fraction of perfect palindromes expected (PERF_EXP)
Fraction of perfect palindromes observed (PERF_OBS)
fraction of purine stretches >(R)10 (ADNACC)
Fraction of pyr/pur stretches >(YR)10 (ZDNACC)
G content (GCONTENT)
GC skew (GC_SKEW_LEADOVERLAG)
Global Direct Repeats (100 bp window) (GLO_DIR_REPEAT)
Global Inverted Repeats (100 bp window) (GLO_INV_REPEAT)
Ket Skew (KETO_SKEW_LEADOVERLAG)
Length (LENGTH)
Local Direct Repeats (15 bp window) (LOC_DIR_REPEAT)
Local Everted Repeat (15 bp window) (LOC_EVR_REPEAT)
Local Inverted Repeats (15 bp window) (LOC_INV_REPEAT)
Local Mirror Repeats (15 bp window) (LOC_MIR_REPEAT)
Number of 16/18s rRNA (RNAMMER_SSU_COUNT)
Number of 23/28s rRNA (RNAMMER_LSU_COUNT)
Number of 5/8s rRNA (RNAMMER_TSU_COUNT)
Number of ECF sigma factors (SIGMAECF_PROMOTERS_COUNT)
Number of genes (GeneMark Prediction) (NCBI_GENEMARK_NGENES)
Number of genes (Glimmer Prediction) (NCBI_GLIMMER2_NGENES)
Number of genes (Recent Annotation) (NGENES)
Number of secretion Type I Components (SECRETION_TYPEI_COUNT)
Number of secretion Type II Components (SECRETION_TYPEII_COUNT)
Number of secretion Type III Components (SECRETION_TYPEIII_COUNT)
Number of secretion Type IV Components (SECRETION_TYPEIV_COUNT)
Number of secretion Type V Components (SECRETION_TYPEV_COUNT)
Number of Sigma54 factors (SIGMA54_PROMOTERS_COUNT)
Number of tRNAs (GenBank Annotation) (ANN_TRNA_COUNT)
Number of tRNAs (tRNAscan) (TRNA_SCAN_COUNT)
Pseudo-target. MD5 checksum of mysql table explain (TO_GENEWIZDB_MD5)
Quasi-palindromes / perfect pal. ratio (QUASI_RATIO)
Quasi-palindromes observed / quasi-palindromes expected (QUASI_PERF_RATIO)
Quasi-pallindromes expected (QUASI_EXP)
Quasi-pallindromes observed (QUASI_OBS)
Ratio of expected/observed perfect pal. (PERF_RATIO)
Replication oligomer skew - Amplitude (ORISUM_NEWNARROW_AMP)
Replication oligomer skew - Signal/Noise (ORISUM_NEWNARROW_SN)
Simple (short tandem) Repeats (SR_PERCENT)
T content (TCONTENT)
True Proteins (est. from Prot lentgh dis) (TRUE_PROTEINS)
True Proteins / annotated proteins (TRUE_PROT_RATIO)