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GC profile, chromozóm

GC profile, okno 10k, rc.cont.4

GC skew, chromosome

GC skew [(G+C)/(G-C) in sliding window] correlates with direction of the replication. Can be used for identifying of the origin of the replication. Window 50k.

Alternativní: GC, GC skew, GC / AT skew (kumulativní) - chromozóm

Příklad analýzy chromozomální sekvence bakterie Rhodobacter capsulatus SB1003. (a) Profil celkového zastoupení GC (%). Výpočet GC byl proveden po úsecích 10 kb ("plovoucí okno") dle vztahu: nCG/nACGT. Šedý obdélník vyznačuje oblast, kde se obsah GC neliší od průměru o více než 2.5 násobek standardní odchylky. (b) Profil zastoupení G proti C – keto proti amino (GC „skew“). Výpočet byl proveden po úsecích 150 kb dle vztahu: (nC-nG)/(nC+nG). (c) Profil zastoupení keto proti amino bázím (kumulovaný GC a TA „skew“). Výpočet byl proveden kumulativně (Yi = ΣY(1..i)) po úsecích 10 kb a výpočty hodnot Yi dle vztahů: (nC-nG)/(nC+nG) [červená], (nA-nT)/(nA+nT) [modrá]. O / T – počátek / konec replikace.

Interprtace GC / AT skew

Jak interpretovat AT /GC skew.

Sequencing error distribution

Distribution of sequencing errors (mostly identified as frameshifts) along chromosome between rc.chromosome.4 and rc.chromosome.6

Rhodobacter - project map

verze 070315

Functional classes (bars)

Preliminary version of functional classes. This version is only for easily annotated and assigned genes/functions.

Functional classes (pie)

Preliminary version of functional classes. This version is only for easily annotated and assigned genes/functions.

Annotation success

Účinnost anotace v závislosti na parametrech: bit score a similarity over %

[Rhodo] circular map 1: gc, rna and frameshifts

circular map of rhodobacter chromosome (produced by circos): [a] in red: gc content, window 5kb, scale 40-75%; light red slices designate regions with gc < 50% [b] in green: positions of t-rna (dark green) and r-rna (green) [c] in blue: frameshofts distribution (differences between rc.4 and rc.6)

[Rhodo] circular map 2: genes

rhodobacter chromosome: [a] blue and gray: predicted genes in forward and reverse orientation (dark blue: annotation quality high; light blue: annotation quality low; grey: no annotation) [b] red: t-rna (dark red) and r-rna (red) [c] violet: gc content (window 5kb); [d] light red: highlits denote gc < 50%

[rhodo] circular map, region with viruses

rhodobacter chromosome, 09 -1.6 kb: [a] blue and gray: predicted genes in forward and reverse orientation (dark blue: annotation quality high; light blue: annotation quality low; grey: no annotation) [b] red: t-rna (dark red) and r-rna (red) [c] violet: gc content (window 5kb); [d] light red: highlits denote gc < 50%

[Rhodo] Functional classes (bars) v2

Preliminary version of functional classes. This version covers roughly 2/3 of all genes.

[Rhodo] circular map 2: genes v2

rhodobacter chromosome: [a] predicted genes in forward and reverse orientation (blue: cellular processes; yellow: information storage and process; red: metabolism: grey: poorly annotated or no annotation) [b] red: t-rna (dark red) and r-rna (red) [c] violet: gc content (window 5kb)

[rhodo] hits to 42 most similar genomes

outer gray circle: ideogram with rnas and viral parts (red); blue histogram: number of hits to 100 genomes; gray heatmap: quality of the best hit against uniprot; inner circle of marks: rnas; pink sectors: integrated viral parts. generated by hynek strnad

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GC profile, chromozóm

GC profile, plazmid

GC skew, chromosome

GC skew, plasmid

Alternativní: GC, GC skew, GC / AT skew (kumulativní) - chromozóm

Interprtace GC / AT skew

Sequencing error distribution

Rhodobacter - project map

Functional classes (bars)

Functional classes (pie)

Annotation success

[Rhodo] circular map 1: gc, rna and frameshifts

[Rhodo] circular map 2: genes

[rhodo] circular map, region with viruses

[Rhodo] Functional classes (bars) v2

[Rhodo] circular map 2: genes v2

[rhodo] hits to 42 most similar genomes