SEED Viewer Numbers - Revision history

TobiasPaczian: /* SeedViewer */

2007-08-15T17:48:08Z

SeedViewer

TobiasPaczian: /* SeedViewer */

2007-08-15T16:48:41Z

SeedViewer

TobiasPaczian: /* SeedViewer */

2007-08-15T16:46:00Z

SeedViewer

TobiasPaczian: /* MG-RAST */

2007-08-15T16:33:06Z

MG-RAST

TobiasPaczian: /* Numbers in the SeedViewer, RAST Server and MG-RAST Server */

2007-08-15T16:24:15Z

Numbers in the SeedViewer, RAST Server and MG-RAST Server

TobiasPaczian: /* Numbers in the SeedViewer, RAST Server and MG-RAST Server */

2007-08-15T16:23:32Z

Numbers in the SeedViewer, RAST Server and MG-RAST Server

TobiasPaczian at 16:23, 15 August 2007

2007-08-15T16:23:10Z

New page

== Numbers in the SeedViewer, RAST Server and MG-RAST Server ==

The SeedViewer offers you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.

=== MG-RAST ===

On the details page of your organism, you will find the following numbers:

* ''Number of sequences''
: This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database.

* ''Total sequence length''
: This is the sum of the lengths of all submitted sequences.

* ''Average read length''
: This is the '''Total sequence length''' divided by the '''Number of sequences'''

* ''Longest sequence id'
:

* ''Longest sequence length''
:

* ''Shortest sequence id''
:

* ''Shortest sequence length''
:

← Older revision		Revision as of 17:48, 15 August 2007
Line 76:		Line 76:
	: '''hypothetical'''		: '''hypothetical'''
	: This is the number of coding sequences which were assigned to be hypothetical (or a synonym)		: This is the number of coding sequences which were assigned to be hypothetical (or a synonym)
		+
		+	* ''Subsystem Counts''
		+	The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.

@@ Line 62: / Line 62: @@
 * ''Number of Subsystems''
+: The number of different subsystem in which at least one member was found in the fragments of the genome.
 * ''Number of Coding Sequences''
+: The number of protein encoding genes found in the submitted fragments that matched against our database.
 * ''Number of RNAs''
+: The number of RNAs found in the submitted fragments that matched against our database.
 * ''Protein Encoding Genes''

← Older revision		Revision as of 16:46, 15 August 2007
Line 54:		Line 54:

	On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome:		On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome:
		+
		+	* ''Size''
		+	: This is the number of basepairs of sequence of this genome.
		+
		+	* ''Number of Fragments''
		+	: This is the number of fragments which included at least one coding sequence that could be matched to our database.
		+
		+	* ''Number of Subsystems''
		+	:
		+
		+	* ''Number of Coding Sequences''
		+	:
		+
		+	* ''Number of RNAs''
		+	:
		+
		+	* ''Protein Encoding Genes''
		+	: The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left.
		+	: '''non-hypothetical'''
		+	: This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein''
		+	: '''hypothetical'''
		+	: This is the number of coding sequences which were assigned to be hypothetical (or a synonym)

← Older revision		Revision as of 16:24, 15 August 2007
Line 1:		Line 1:
−	~~= Numbers in the~~ SeedViewer, RAST Server and MG-RAST Server =	+	The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.
−
−	~~The SeedViewer offers~~ you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.

	=== MG-RAST ===		=== MG-RAST ===

← Older revision		Revision as of 16:23, 15 August 2007
Line 1:		Line 1:
−	== Numbers in the SeedViewer, RAST Server and MG-RAST Server ==	+	= Numbers in the SeedViewer, RAST Server and MG-RAST Server =

	The SeedViewer offers you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.		The SeedViewer offers you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.

@@ Line 15: / Line 15: @@
 * ''Longest sequence id'
+: This is the identifier string of the longest sequence submitted.
 * ''Longest sequence length''
+:
-* ''Shortest sequence id''
+* ''Divergent overlaps''
+:
-* ''Shortest sequence length''
+* ''Same strand overlaps''
+: