Difference between revisions of "MG-RAST Numbers"
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| + | The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. The purpose of this page is to explain how we calculate these numbers and what they mean. | ||
| + | |||
| + | |||
=== MG-RAST === | === MG-RAST === | ||
| − | On the details page of your | + | On the details page of your MG-Rast job, you will find the following numbers: |
* ''Number of sequences'' | * ''Number of sequences'' | ||
| − | : This is the total number of sequences submitted by the user for this | + | : This is the total number of sequences submitted by the user for this metagenome. 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'' | * ''Total sequence length'' | ||
| − | : This is the sum of the lengths of all submitted sequences. | + | : This is the sum of the lengths (bp) of all submitted sequences. |
* ''Average read length'' | * ''Average read length'' | ||
| − | : This is the | + | : This is the ''Total sequence length'' divided by the ''Number of sequences'' |
| − | * ''Longest sequence id' | + | * ''Longest sequence id'' |
: This is the identifier string of the longest sequence submitted. | : This is the identifier string of the longest sequence submitted. | ||
* ''Longest sequence length'' | * ''Longest sequence length'' | ||
| − | : This is the length of the longest sequence submitted. | + | : This is the length (bp) of the longest sequence submitted. |
* ''Shortest sequence id'' | * ''Shortest sequence id'' | ||
| Line 25: | Line 28: | ||
| − | === SeedViewer === | + | === SeedViewer - Overview === |
| − | On the '' | + | On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome: |
* ''Size'' | * ''Size'' | ||
| − | : This is the number of basepairs of sequence | + | : This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome. |
| + | |||
| + | : '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size. | ||
* ''Number of Fragments'' | * ''Number of Fragments'' | ||
| − | : This is the number of | + | : This is the number of submitted sequences which included at least one coding sequence that could be matched to our database. |
* ''Number of Subsystems'' | * ''Number of Subsystems'' | ||
| − | : The number of different | + | : The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome. |
* ''Number of Coding Sequences'' | * ''Number of Coding Sequences'' | ||
: The number of protein encoding genes found in the submitted fragments that matched against our database. | : The number of protein encoding genes found in the submitted fragments that matched against our database. | ||
| + | : '''Note:''' This number may be higher than the ''Number of Fragments'' if there are multiple matches on a single fragment. | ||
* ''Number of RNAs'' | * ''Number of RNAs'' | ||
| Line 45: | Line 51: | ||
* ''Protein Encoding Genes'' | * ''Protein Encoding Genes'' | ||
| − | : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) | + | : The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) |
| − | : | + | : * ''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'' | : 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) | : This is the number of coding sequences which were assigned to be hypothetical (or a synonym) | ||
| + | |||
| + | : '''Known bug:''' In some cases coding sequences do not have any functional assignment, but are not counted as hypothetical protein. That causes the number of hypothetical and non-hypothetical coding sequences not to add up to the total number of fragments. | ||
* ''Subsystem Counts'' | * ''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 | + | : 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:''' Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times). | ||
| + | |||
| + | |||
| + | === SeedViewer - Taxonomy === | ||
| + | |||
| + | The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment. | ||
| + | |||
| + | We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database. | ||
Latest revision as of 10:13, 3 October 2007
The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your metagenome. 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 MG-Rast job, you will find the following numbers:
- Number of sequences
- This is the total number of sequences submitted by the user for this metagenome. 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 (bp) of all submitted sequences.
- Average read length
- This is the Total sequence length divided by the Number of sequences
- Longest sequence id
- This is the identifier string of the longest sequence submitted.
- Longest sequence length
- This is the length (bp) of the longest sequence submitted.
- Shortest sequence id
- This is the identifier string of the shortest sequence submitted.
- Shortest sequence length
- This is the length of the shortest sequence submitted
SeedViewer - Overview
On the Metagenome Overview page, there are a number of statistical counts about the selected metagenome:
- Size
- This is the number of basepairs (total length) of all of the sequences submitted for a given metagenome.
- Known bug: Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size.
- Number of Fragments
- This is the number of submitted sequences which included at least one coding sequence that could be matched to our database.
- Number of Subsystems
- The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome.
- Number of Coding Sequences
- The number of protein encoding genes found in the submitted fragments that matched against our database.
- Note: This number may be higher than the Number of Fragments if there are multiple matches on a single fragment.
- Number of RNAs
- The number of RNAs found in the submitted fragments that matched against our database.
- Protein Encoding Genes
- The numbers are given in absolute and percent value. They should add up to 100% (given rounding error)
- * 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)
- Known bug: In some cases coding sequences do not have any functional assignment, but are not counted as hypothetical protein. That causes the number of hypothetical and non-hypothetical coding sequences not to add up to the total number of fragments.
- 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: Not every coding sequence is part of a subsystem and a single coding sequence may fulfill functional roles in more than one subsystem (and thus be counted multiple times).
SeedViewer - Taxonomy
The taxonomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment.
We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database.