You can add individual DNA properties from the scroll-down box to the left (e.g. Intrinsic Curvature, Stacking Energy etc) or you can select DNA properties from one of the standard atlas types (e.g. GENOME ATLAS, STRUCTURE ATLAS). Selecting a standard atlas type will clear the properties already included (shown in the middle table)

(click a DNA property to see explanation)

BLAST LANES BLAST LANES

This section allows to defined up to 7 BLAST lanes against the selected reference. Click the links 'Add new BLAST lane' and 'Remove this lane' to add and remove lanes.

BLAST LANE NO. 1

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 1
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

BLAST LANE NO. 2

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 2
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

BLAST LANE NO. 3

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 3
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

BLAST LANE NO. 4

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 4
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

BLAST LANE NO. 5

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 5
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

BLAST LANE NO. 6

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 6
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

BLAST LANE NO. 7

	Database proteins/ORFs in fasta format directly from your local disk:
- or	Select Genome Project	Search:: ()
	Legend	Blast lane 7
	Fixed data range:	From: To:
- or -	choose standard deviation around mean:	Local Global
	From:
	To:	Color scale:
	Via: (optional)
	Algorithm:

Remove this lane

Add new BLAST lane

PSEUDO GENES / CUSTOM ANNOTATIONS PSEUDO GENES / CUSTOM ANNOTATIONS

Annotations of pseudo-genes or miscellaneous features can be provided in the input field to the right (features 'misc' and 'Pseudo' are accepted). Annotation of pseudo-genes in prokaryotes are downloaded from http://www.pseudogenes.org and can be searched by clicking 'Query pseudo-genes'. Please visit www.pseudogenes.org, to see which genomes are available. You may also provide a custom annotation. Click 'Insert example' to see an example annotations.

MAPPING SHORT SEQUENCING READS MAPPING SHORT SEQUENCING READS

This secction allows to upload a fasta file containing sequencing and qual files containing the quality measures. Three measures are derived from the reads: The weighted coverage, derivied from BLAST search against the reference genome, plus average and maximum uniqueness-weighted quality measure.

Source files

Read sequences (fasta)

Example FNA file

Read QUAL file (optional)

Example QUAL file

Large contigs (optional)

Example FNA file

Show weighted coverage (-readLaneCov)

Shows the position specific coverage weighted for uniqueness


-3sd	+3sd

Show read agreement with reference (-readLaneAgr)

A boolean (0 .. 1) indicating if the base with the highest frequency match/agrees with the reference nucleotide


0.0	1.0

Show maximum uniqueness (-readLaneMax)

This measure show the maximum obtained uniqueness weighted quality at each position


-3sd	+3sd

Show information content (-readLaneInf)

When all reads are mapped to the reference, the information measure (0 .. 2 bits) are calculated. 0 meaning equal distribution of ATGC, and 2 meaning a fully conserved nucleotide


0.0	2.0

Show read absence (-readLaneAbs)

The number of alignments present at each position. The scale only shows values from 0 to 1. Zero (black) meaning reads are absent, values at 1 or above meaning that reads are present


0.0	1.0

Read clipping range (-clipfrom and -clipto)

Clip reads and qualities in specified range (0 .. 0 means no clipping).

Only map perfect match positions (-o)

When read has been aligned, the quality values are mapped to the genome postion. Enabling this option will prevent adding quality measure for mismatch positions.

Continue mapping reads with BLAST score of (-i)

For a given read, all hits found in the genome will be included as long as the BLAST score is bigger than this fraction times the highest BLAST score obtained for that read.

Default quality value (-j)

If quality values are missing, this number will be used instead.

Hit identity fraction (-k)

Include only hits with better (higher) BLAST score of this value.

Hit E-value (-e)

Include only hits with better (lower) E-value than this. This is the initial filtering step, and affects the run-time significantly. Increasing the E-value greather than 1 ·10^-5 has no effect.

CUSTOM LANES CUSTOM LANES

This section allows to defined up to custom. This requires a uploaded data file (one line / number per nucleotide position). Click the links 'Add new custom lane' and 'Remove this lane' to add and remove lanes.

CUSTOM LANE NO. 1

Custom data (one line/number per base pair):
Legend	Custom lane 1
Fixed data range:	From: To:
-or- choose standard deviation around mean:	Local Global
From:
To:	Color scale:
Via: (optional)

Remove this lane

Add new custom lane

CUSTOM LANE NO. 2

Custom data (one line/number per base pair):
Legend	Custom lane 2
Fixed data range:	From: To:
-or- choose standard deviation around mean:	Local Global
From:
To:	Color scale:
Via: (optional)

Remove this lane

Add new custom lane

CUSTOM LANE NO. 3

Custom data (one line/number per base pair):
Legend	Custom lane 3
Fixed data range:	From: To:
-or- choose standard deviation around mean:	Local Global
From:
To:	Color scale:
Via: (optional)

Remove this lane

Add new custom lane

CUSTOM LANE NO. 4

Custom data (one line/number per base pair):
Legend	Custom lane 4
Fixed data range:	From: To:
-or- choose standard deviation around mean:	Local Global
From:
To:	Color scale:
Via: (optional)

Remove this lane

Add new custom lane

CUSTOM LANE NO. 5

Custom data (one line/number per base pair):
Legend	Custom lane 5
Fixed data range:	From: To:
-or- choose standard deviation around mean:	Local Global
From:
To:	Color scale:
Via: (optional)

Remove this lane

Add new custom lane

MY RUNS (0) MY RUNS (0)

(no stored sessions)

GETTING HELP

Scientific questions:

This file was last modified Wednesday 12th 2014f March 2014 13:43:15 GMT

A Content
T Content
G Content
C Content
AAAA
TTTT
GGGG
CCCC
Palindromic hexamers
T4 or C4 vs. A4 or G4
(CR) dinuc. vs. (YG) dinuc.
(Y)10 vs. (R)10
(CR)5 vs. (YG)5
(CA)3
(CG)3
(TA)3
(TG)3
(YR)5
Intrinsic Curvature
Stacking Energy
Position Preference
Percent AT
GC Skew
AT Skew
DNase I Sensitivity
Propeller Twist
Direct Repeats
Everted Repeats
Local Inverted Repeats
Mirror Repeats
Simple Repeats
Global Inverted Repeats
Global Direct Repeats
Protein Deformability
Quasi-palindromes
Perfect-palindromes
SIDD, s:-0.055
SIDD, s:-0.045
SIDD, s:-0.035