CoGe Blast

CoGe Blast's page is shown above. Here you can enter your sequence(s) in a text box, select the type of blast search you wish to perform, chose which organism(s) you which to search, and specify blast options. For this example, you will start by only searching the maize genome. Follow the numbered boxes to configure and run a CoGe Blast analysis:

What does "Zea mays" really mean? To find out the exact content of one of these genomes, press the "Get Org Info" button which is located below the organism list. (Unfortunately that button is not show in this version of CoGe Blast, but is present in the current version.)


CoGe Blast Results


The time it takes to get results depends on the number of organisms searched, the size of their genomes, and the number of HSPs (i.e. high-scoring sequence pairs or Blast hits) returned. When the results are being generating, you will see a spinning double helix on the top of the web-page and, when finished, this will be replaced by your results. The settings that you used for the Blast analysis will still be available below the results in order to make it easy for you to reconfigure your analysis and generate new results.

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The Blast results are organized graphically to make finding and navigating through blast hits easy. On the left of the image is an overview of the genomic segments (e.g. chromosomes, contigs) with HSPs identified by triangles and lines. On the right is a list of HSPs and any genomic feature (e.g. gene) that they overlap. In this example, three HSPs were identified that overlap two unique genomic features.

A nice feature of CoGe Blast is the ability to evaluate HSPs in their genomic context. This is useful for identifying genomic features that are close homologs, orthologs, paralogs, etc. To evaluate an HSP simply click on an arrow in the genomic visualization or on an HSP number in the HSP list(s):

HSP information gets displayed in the middle of the results section and is broken down into three sections:

  1. 1.The query sequence HSP coverage (the sequence you used to search)

  2. 2.An overview of the HSP in the context of the genome (including some surrounding sequence)

  3. 3.A summary of the HSP statistics.

This integrated view will also show you other HSPs that matc
h in the visualized genomic region. The HSP that you clicked on is colored yellow (HSP 1, in this example) and other HSPs are colored red (HSP 2). As can be seen in the figure above, HSP 1 covered most of the query sequence and matched the 3' region of an annotated gene in the genomic region. Also, HSP 2 is shown which covers most of the query sequence not covered by HSP 1 and matched the 5' end of the same annotated gene. This type of visualization can make it very easy to evaluate which features with overlapping HSPs are of interest. In this case, since you are searching for your sequence in the maize genome, this feature (AC191091.1_FG018) may be your sequence. You can easily exam HSP 3 the same way (image on right). From this view, you can see that there is minimal coverage of the query sequence and that the overlapping feature is not of interest in your analysis.


If you look at the HSP statistics, you can see that for HSP 1, the query sequence is only 94% identical to the genomic sequence. This means that although you had very high coverage, this feature is not the same as the query. Since maize is a recent tetraploid, there will be a very close paralog in maize for many genes. Combined with the fact that the maize genome sequence is not yet finished, there is a good chance that this sequence has not yet been assembled into the maize genome. Thus you can conclude that although you did not found your specific sequence in this set of maize sequences, you did find a close paralog that perhaps was derived from maize's most recent tetraploidy event. To investigate this, you'll need to find orthologs to this sequence in related grass species and perform some comparative genomics analyses to identify synteny.


Please keep in mind that CoGe updates all in-progress genomes periodically, so visit maize again if the first query does not meet expectations.