autoSNPdb Help Pages
This is a guide for using autoSNPdb. If you can't find what you need here then please look up our FAQ
Click on a link below to view help for that topic.

Keyword Search

<-Keyword Search Display->
Species Name

The species name that was selected on the first screen appears at the top of this search box.

1. Select search...

Descriptions - With SNPs or Descriptions - All
Searches for any words that you enter in the annotation descriptions of contigs or singletons.
With SNPs just returns those contigs/singletons that have 1 or more SNPs.
Contig ID
Enter a single number to display all of the contigs with that number across all of the assemblies.
When a contig is listed it is shown as <-Contig ID Image->, with the assembly ID and cluster ID at the end.
This is so you can access permanent contigs across different assemblies.
You can return to this contig in ContigView by replacing the numbers in the url, for example autoSNPdb/ContigView.jsp?species=barley&analysisID=1&clusterID=1&contigID=1
Sequence Accession
Enter a sequence accession, for example BQ469510, to retrieve the contig or singleton that the sequence is a member of.
Gene Ontology - With SNPs or Gene Ontology - All
Similar to the Description search, except this searches for any words that you enter in the Gene Ontology annotation of contigs or singletons.
Again, With SNPs just returns those contigs/singletons that have 1 or more SNPs.

2. Display options...

Choosing Extended Display shows all of the annotation for each contig/singleton, whereas Concise Display shows just the primary annotation. Both cases highlight matches with the words entered, and it has no impact on the number of records displayed on each screen.
Extended:
<-Extended Display->
Concise:
<-Concise Display->

SNP Image

For details of the AutoSNP calculations such as weighted cosegregation, see

Barker G, Batley J, O'Sullivan H, Edwards KJ and Edwards D. (2003) Redundancy Based Detection of Sequence Polymorphisms in Expressed Sequence Tag Data using AutoSNP. Bioinformatics 19:421-422

Line Height
The line height represents the SNP score for the SNP at that position. The SNP score is the number of sequences containing the SNP at that position.

Notice that the possible range has been divided into four parts and that the scale given is logarithmic. The top line will represent the maximum SNP score calculated for any SNP in the contig.

SNP scores are always whole numbers
If the top of the line meets the guide at 2.9 then the SNP score will be 3!!!
 
<-SNP Image->
Line Positioning
Each line is positioned according to the location of the SNP it represents. The black line at the bottom of the image represents the entire contig.

When the mouse is held over a line, more detailed information about that SNP will be displayed.

If you click on a line you will be taken to the corresponding position in the SNP summary.
  Line Colour
1.0







0.0
<-Heat Map->   The colour of a line represents the weighted cosegregation score of the corresponding SNP.

The cosegregation score is a measure of the number of SNPs in the alignment which share the same pattern of polymorphism between aligned sequences. The weighted cosegregation score takes account of missing data in the alignment of ESTs that may otherwise bias the cosegregation score.

Back To Top

Changing Views

<-Changing views - Sequences-> Clicking on this link shows the screen as at Alignment.
<-Changing views - Summary-> Clicking on this link shows the screen as at Summary.

Back To Top

Changing Labels

<-Change Label->
You can change the annotation in the labels (the left-hand column beside the sequences).

Simply click on the Cultivar link.
The labels cycle through Cultivar - Accession - DevStage - Tissue - Cultivar.

The link shows the label that is currently showing.
The Icon QM brings up help about the Abbreviations used, or you can get to it here.

Back To Top

Alignment

<-Sequence Alignment Guide->
The numbers along the top are positions in the consensus sequence.
The sequence above the top line is the consensus sequence produced by CAP3.
Aligned EST sequences appear one after another below the consensus sequence and SNPs are highlighted in one of four colours representing each of the four bases. All SNPs and indels are outlined in red.

Some sequences have been clipped and the clipped sequence part has a grey background. Whether or not a sequence has been clipped is determined by CAP3. SNPs which lie completely within a clipped region are not counted. In the case where a SNP contains some clipped sequence, the clipped bases do not contribute to the SNP score or the weighted cosegregation score.

Back To Top

Summary

Summary Guide This shows just the SNPs in the alignment.

The numbers at the top (rotated) are the position in the consensus sequence.


Show Sequence

Click Show to see the consensus sequence.

<-Show Sequence->

Back To Top

SNP Information

Click the plus to show details of the SNPs.

<-SNP Information->

Back To Top

EST Sequence Information

Click the plus to show details of the EST sequences.

Click on the Name to open the full GenBank record for that sequence in a new window.
EST Sequence Information

Back To Top

UniRef Annotation

Click the plus to show details of the UniRef Annotations.

Click on the Name to open the full UniRef record for that sequence in a new window.
<-UniRef Annotation->

Back To Top

GenBank Annotation

Click the plus to show details of the GenBank Annotations.

Click on the Name to open the full GenBank record for that sequence in a new window.
<-GenBank Annotation->

Back To Top

Gene Ontology Annotation

Click the plus to show details of the Gene Ontology Annotations.

Click on the GO Accession to open the full AmiGO record for that term in a new window.
<-Gene Ontology Annotation->

Back To Top

Reference Genome Annotation

Click the plus to show details of the Reference Genome Annotations.

Click on the Region to open the full Gramene record for that region in a new window.
<-Reference Genome Annotation->

Back To Top